Chimpanzees and bonobos are the organisms most closely related to humans among all living species. These two African apes share a common ancestor with us that lived roughly five to eight million years ago, and our genomes overlap to a degree unmatched by any other creature on the planet. But the question of relatedness extends far beyond our nearest ape cousins, and the answer changes depending on how far back you zoom: through gorillas and orangutans, past monkeys and lemurs, beyond mammals entirely, and eventually into a world of single-celled organisms that set the stage for animal life itself.
Chimpanzees and Bonobos Share the Top Spot
For decades, chimpanzees were considered our sole closest relative. That picture became more nuanced when the bonobo genome was sequenced and compared directly with both chimpanzee and human DNA. The study found that more than three percent of the human genome is actually more closely related to either the bonobo or the chimpanzee genome than those two ape genomes are to each other.1PubMed Central. The bonobo genome compared with the chimpanzee and human genomes In other words, some stretches of your DNA look more “bonobo” than “chimp,” and vice versa. This patchwork pattern is a consequence of how populations split gradually rather than all at once millions of years ago.
How similar are human and chimpanzee genomes overall? The famous “99 percent identical” figure, still widely repeated, is a simplification. When researchers counted not just single-letter differences in DNA but also insertions, deletions, and duplicated segments, the total divergence came to roughly four percent, comprising about 35 million single-letter changes and around 90 million base pairs worth of insertions and deletions.2PubMed. Comparing the human and chimpanzee genomes: searching for needles in a haystack Even at four percent, chimpanzees and bonobos remain overwhelmingly our closest genetic match among living species. By comparison, any two unrelated humans differ by only about 0.1 percent.
The split between the human lineage and the lineage leading to chimps and bonobos was not a clean break. Genomic analyses suggest the divergence began around six million years ago, but some regions of the genome show signs of gene flow between the two populations well after the initial split.3PubMed Central. ‘Chumanzee’ evolution: the urge to diverge and merge Estimates of the timing range from about five million years ago to as far back as seven or eight million, depending on which parts of the genome are examined and which calibration points are used.4PubMed Central. Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution
Gorillas and Orangutans Come Next
After chimpanzees and bonobos, gorillas are our closest living relatives. Their lineage branched off from the line leading to humans and chimps roughly one and a half to two million years before the human-chimpanzee split, placing the gorilla divergence at somewhere around six to eight million years ago.5PubMed Central. Insights into hominid evolution from the gorilla genome sequence Average sequence divergence between humans and gorillas is about 1.6 percent, compared with roughly 1.2 percent between humans and chimpanzees.6PubMed. Chromosome phylogenies of man, great apes, and Old World monkeys
Gorilla genomics has a twist that surprises many people. In about 30 percent of the genome, the gorilla sequence is actually closer to the human or chimpanzee sequence than those two are to each other.5PubMed Central. Insights into hominid evolution from the gorilla genome sequence This does not mean gorillas are sometimes our closest relative instead of chimps. It reflects a phenomenon called incomplete lineage sorting, where genetic variation that existed in the ancestor of all three species got shuffled randomly into different descendant lineages. The effect is less common around genes that code for proteins, which suggests natural selection has been shaping the functional parts of great ape genomes throughout this entire period.
Orangutans sit one step further out. Their lineage diverged from the African ape and human lineage roughly 12 to 16 million years ago. The average sequence divergence between humans and orangutans is about three percent, roughly two and a half times the gap between humans and chimps. A similar pattern of incomplete lineage sorting shows up here too, though at much lower levels: about one percent of the human genome is more closely related to the orangutan genome than to the chimpanzee genome, a relic of the large, genetically diverse ancestral population that gave rise to all three lineages.7PubMed Central. Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection
Our Extinct Closest Kin
Living species are not the whole story. If you could rewind the clock just a few hundred thousand years, you would meet relatives far closer to us than any chimpanzee. Neanderthals and Denisovans were hominins whose lineage separated from modern humans an estimated 400,000 to 800,000 years ago.4PubMed Central. Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution That is a tiny fraction of the time separating us from chimpanzees. Ancient DNA recovered from bones has shown that these groups were close enough to interbreed with modern humans, and most people of non-African descent carry a small percentage of Neanderthal DNA today.
Neanderthals and Denisovans themselves split from each other not long after their shared lineage diverged from ours. Population modeling suggests the Neanderthal-Denisovan lineage shrank to a small size just after separating from modern humans, then the two groups went their separate ways, with Neanderthals going on to form a large and geographically subdivided population across western Eurasia.8PubMed Central. Early history of Neanderthals and Denisovans Researchers have been able to study specific genetic variants carried by both Neanderthals and Denisovans and test their biological effects in living organisms, finding that some of these ancient variants influence anatomical development in ways that help explain physical differences between archaic and modern humans.9PubMed Central. A Neanderthal/Denisovan GLI3 variant contributes to anatomical variations in mice
Gibbons, Monkeys, and the Wider Primate Family
Beyond the great apes, the next branch out leads to the gibbons, also called lesser apes or hylobatids. Gibbons are small, long-armed, spectacularly acrobatic primates found across Southeast Asia. They share with great apes and humans a roughly similar timeline of diversification, but their faces and skulls are far less varied than those of the great ape family. Research comparing craniofacial diversity in great apes versus gibbons found that hominids (the group including great apes and humans) show much higher skull diversity than hylobatids, despite similar levels of genetic differentiation. The radiation that produced this diversity coincides with the roughly seven-million-year-old split between human and chimpanzee lineages.10PubMed Central. Accelerated evolution increased craniofacial divergence between humans and great apes
Further out still, Old World monkeys (like baboons, macaques, and vervet monkeys) share a common ancestor with apes that lived roughly 25 to 30 million years ago. New World monkeys (like spider monkeys and marmosets) diverged even earlier. Chromosomal comparisons between humans, great apes, and these monkey groups reveal a tidy pattern: humans and great apes differ by only a handful of chromosomal rearrangements, while the differences pile up as you compare more and more distantly related primates, tracing a path backward through successively older common ancestors.6PubMed. Chromosome phylogenies of man, great apes, and Old World monkeys One well-known example: humans have 46 chromosomes while all other great apes have 48, because two ancestral chromosomes fused into human chromosome 2 sometime after our lineage split from chimpanzees.
The Closest Non-Primate Relatives
Once you step outside the primate order, the identity of our nearest relatives becomes less obvious. Two groups of small, obscure mammals have been at the center of this debate: colugos (sometimes called “flying lemurs,” though they neither fly nor are lemurs) and tree shrews (small, squirrel-like creatures found in Southeast Asian forests). Molecular evidence consistently places tree shrews, colugos, and primates together in a larger group on the mammalian family tree.11PubMed Central. Colugos: obscure mammals glide into the evolutionary limelight
The trickier question is how these three groups relate to one another internally. For a time, colugos appeared to be the sister group of primates, which would have made them our closest non-primate relatives. More recent chromosomal and genetic analyses have shifted the picture. Evidence from molecular cytogenetics suggests that colugos and tree shrews are more closely related to each other than either is to primates, forming their own sister pair.12PubMed Central. Flying lemurs–the ‘flying tree shrews’? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade A large-scale phylogenomic study using thousands of genetic markers supports tree shrews as the sister group to the colugo-primate grouping, though it could not completely rule out a closer link between tree shrews and rodents plus rabbits.13PubMed Central. Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements The exact branching order remains genuinely uncertain, which is a reminder that some parts of the evolutionary tree are still being debated even with modern genomic tools.
How Far Back Does Relatedness Go?
Relatedness does not stop at mammals. Every animal on Earth shares common ancestry with humans if you go back far enough, and the question of “which organisms are most closely related” can be asked at every scale.
Among vertebrates, for instance, the closest living relatives of all land vertebrates (amphibians, reptiles, birds, and mammals, collectively called tetrapods) are the lungfish. This was debated for over a century, with the coelacanth once considered the stronger candidate. Multiple independent molecular studies have now settled the question in favor of lungfish, with analyses of nuclear protein-coding genes supporting lungfish as the closest living aquatic relatives of tetrapods with high statistical confidence.14PubMed Central. Nuclear protein-coding genes support lungfish and not the coelacanth as the closest living relatives of land vertebrates Some analyses have found that lungfish and coelacanths actually form a single group that together is the nearest living relative of land vertebrates.15PubMed Central. 43 genes support the lungfish-coelacanth grouping related to the closest living relative of tetrapods with the Bayesian method under the coalescence model Either way, when you look at a lungfish, you are looking at the closest living echo of the fish that first hauled itself onto land hundreds of millions of years ago.
Zoom out further and you reach the base of the chordates, the group that includes all vertebrates plus animals like sea squirts and lancelets. The closest relatives of chordates are not other complex body-plan animals like insects or worms. They are echinoderms (sea stars, sea urchins) and hemichordates (acorn worms), which together form a group that molecular and morphological evidence consistently places as the sister lineage to chordates.16PubMed. Deuterostome phylogeny and the sister group of the chordates: evidence from molecules and morphology17PubMed. Molecular phylogeny and divergence times of deuterostome animals This means that, in evolutionary terms, a sea urchin is a closer relative of yours than a fruit fly is.
Fungi Are Closer to Us Than Plants
One of the most counterintuitive findings in evolutionary biology is that mushrooms are more closely related to humans than daisies are. Animals and fungi form a single evolutionary group to the exclusion of plants. Evidence from multiple protein comparisons shows animals and fungi clustering together as sister groups, with plants representing an independent lineage that split off earlier.18PubMed. Animals and fungi are each other’s closest relatives: congruent evidence from multiple proteins This overturns older classification systems that grouped fungi with plants simply because both are rooted in place and have cell walls.
The animal-fungus relationship has practical implications. It helps explain why fungal infections are so hard to treat: because fungal cells are biochemically more similar to our own cells than bacterial cells are, drugs that kill fungi tend to also harm human tissue. It also means that between the two organisms growing in your garden, the mushroom is your genealogical cousin and the rosebush is the more distant relation.
Single-Celled Relatives of Animals
Before animals existed, our ancestors were single-celled. The closest living single-celled relatives of all animals are the choanoflagellates, tiny aquatic organisms that feed by waving a whip-like flagellum surrounded by a collar of finger-like projections. As one description puts it, choanoflagellates are to all animals what chimpanzees are to humans: the nearest surviving branch on the family tree.19Cell Press (Current Biology). Quick Guide: Choanoflagellates Choanoflagellates look strikingly similar to the collar cells that line the internal chambers of sponges, which are themselves the most ancient surviving animal lineage. Studying choanoflagellates gives researchers a window into what the single-celled ancestor of all animals may have looked like and how the leap to multicellularity may have happened.
The Deepest Roots of All
Push the question of relatedness all the way to its limit and you arrive at the origin of complex cells themselves. Every cell in your body is a eukaryotic cell, meaning it has a nucleus and internal compartments. The two components of eukaryotic cells trace to two profoundly different lineages. The host cell that became the ancestor of all eukaryotes appears to have been an archaeon, a member of a domain of single-celled organisms distinct from bacteria. Recent genomic work has identified a group of archaea called the Asgard archaea as the closest known living relatives of the archaeal host from which eukaryotes evolved. Asgard archaea carry genes previously thought exclusive to eukaryotes, involved in processes like cellular trafficking, protein recycling, and building an internal skeleton, and growing evidence shows these proteins function in ways that mirror their eukaryotic counterparts.20PubMed Central. The archaeal roots of eukaryotic life
The other piece of the puzzle is the mitochondrion, the energy-producing compartment inside nearly every eukaryotic cell. Mitochondria are of unquestioned bacterial ancestry, descending from an ancient alphaproteobacterium that was engulfed by (or partnered with) the archaeal host cell billions of years ago.21PubMed Central. Mitochondrial evolution This merger produced the first eukaryotic cell, and every animal, plant, fungus, and protist alive today is a descendant of that partnership.22Current Biology. The Origin and Evolution of Mitochondria So in the most literal sense, you carry the legacy of two ancient microbial lineages in every cell of your body: an archaeal host and a bacterial passenger that became permanent.
Why “Percent Similarity” Can Be Misleading
Headlines love to announce that humans share 60 percent of their DNA with bananas or 70 percent with sea sponges. These numbers are real in a narrow technical sense, but they measure something different from what most people assume. When researchers compare highly conserved genes that perform basic cellular housekeeping (copying DNA, building proteins, generating energy), a large proportion of the sequence is identical across almost all life on Earth. Those shared stretches reflect a common origin billions of years ago, not a special closeness to bananas.
The figures that matter for gauging relatedness are the ones that compare genomes comprehensively and account for all types of genetic change: single-letter substitutions, insertions, deletions, duplications, and rearrangements. Even then, the numbers shift depending on what is counted. For humans and chimpanzees, the figure is either about 1.2 percent divergence (counting only single-letter changes in aligned DNA) or about four percent (including structural changes).2PubMed. Comparing the human and chimpanzee genomes: searching for needles in a haystack Both numbers are correct; they just measure different things. The “99 percent” figure is not wrong so much as incomplete, and it can give the misleading impression that the genetic difference between a human and a chimp is trivially small. A four percent difference spread across three billion base pairs still amounts to tens of millions of genetic changes, many of which have profound biological consequences.
Percent similarity also fails to capture the patchwork nature of genome evolution. Because ancestral populations were genetically diverse, different chunks of DNA can tell different evolutionary stories. The finding that 30 percent of the gorilla genome is closer to the human or chimpanzee genome than those two are to each other5PubMed Central. Insights into hominid evolution from the gorilla genome sequence does not mean gorillas are sometimes our closest relative. It means the tree of species relationships and the tree of individual gene histories are not always the same tree. When divergence times are close together, this mosaic pattern is expected, and it is one of the reasons pinning down exact divergence dates remains so difficult.
What Relatedness Does and Does Not Tell Us
Knowing which organisms are closest to humans on the evolutionary tree tells you about shared ancestry, but it does not automatically tell you about shared traits. Bonobos and chimpanzees are equally close to us genetically, yet bonobos are famously less aggressive and more sexually egalitarian than chimpanzees. Gorillas are our next closest relatives, but their social structure, diet, and body plan are dramatically different from ours in ways that the relatively modest genetic distance would not predict.
Conversely, organisms very distant from us on the tree of life can share striking similarities due to convergent evolution. Octopuses have complex eyes with lenses, irises, and retinas that function much like ours, yet the last common ancestor we shared with octopuses lived over 500 million years ago and almost certainly had nothing of the sort. Relatedness tracks genealogy, not resemblance. Two organisms can look alike without being close relatives, and close relatives can look and behave very differently.
That said, close evolutionary kinship does carry practical weight. The fact that chimpanzees are our nearest relatives makes them invaluable for understanding human disease, though ethical concerns have sharply curtailed their use in research. The closeness of fungi to animals explains why antifungal drugs are harder to develop than antibiotics. And the discovery that Asgard archaea are our deep cellular relatives has reshaped how biologists think about the origin of complex life, turning what was once a yawning gap between simple and complex cells into something that looks more like a gradual accumulation of features within a single archaeal lineage.