The Evolution of Rabbits: From Ancient Ancestors to Today

Rabbits split from the lineage that gave rise to rodents roughly 65 million years ago, near the boundary between the Cretaceous and Paleogene periods, and have been diversifying ever since. That places the origin of the rabbit branch of the mammalian family tree in the same geological moment that wiped out the non-avian dinosaurs, an opening that let small mammals radiate into a stunning range of ecological roles. The story from that ancient divergence to the pet in your living room winds through continental drift, ice ages, viral arms races, and at least one island giant the size of a dog.

The Split From Rodents

People commonly assume rabbits are rodents, and it is easy to see why: they are small, furry, and have prominent front teeth. But rabbits belong to a separate order, Lagomorpha, which diverged from the rodent lineage deep in the past. Molecular dating using multiple nuclear genes places the split between rodents and lagomorphs right around the Cretaceous-Paleogene boundary, roughly 65 million years ago, with the earliest divergences among placental mammals reaching back into the Late Cretaceous.¹ Both orders belong to a larger group called Glires, reflecting their shared ancestry, but they have been on independent evolutionary paths for tens of millions of years.

One visible difference hides in the mouth: rabbits have a small second pair of upper incisors tucked behind the larger front ones, a trait rodents lack. That double-incisor arrangement is ancient and shows up in some of the earliest fossils that sit near the base of the lagomorph family tree.

The Earliest Known Ancestors

The oldest fossils that paleontologists can confidently link to the lagomorph lineage come from Asia. Among the most informative is Gomphos, a small mammal from what is now Mongolia, dating to the early Eocene (around 55 million years ago). Gomphos shares several distinctive ankle-bone features with later lagomorphs and differs from rodents in telling ways, making it a strong candidate for a stem lagomorph, meaning it sits on the branch leading to rabbits and hares but predates the modern group itself.² Its foot bones, for instance, are more lagomorph-like than rodent-like, even though its skull still retains some primitive features such as two pairs of lower incisors, something modern rabbits have lost.

Another early relative, Mimolagus, shares many of the same foot-bone traits as Gomphos and is similarly placed as a stem taxon to Lagomorpha. Together, these fossils paint a picture of a group that was already experimenting with the body plan we associate with rabbits, including elongated hind limbs and a hopping-capable ankle, well before the modern family Leporidae appeared.

Out of Asia and Across the Continents

The family Leporidae, which includes all living rabbits and hares, traces its roots to Asia and began spreading outward during the dramatic environmental upheavals of the Cenozoic. The evolutionary history of Leporidae dates back to the Eocene and is tightly linked to global tectonic shifts and climate changes. Their radiation across Europe and North America accelerated after the major turnover in terrestrial ecosystems at the Eocene-Oligocene boundary, about 34 million years ago, when cooling temperatures and the expansion of grasslands opened up new habitats.³

This timing matters because it coincides with a broader reshaping of terrestrial life. Forests were shrinking, grasslands were expanding, and the mammals that could exploit open, drier environments had a profound advantage. Lagomorphs divided into two surviving families: the Leporidae (rabbits and hares) and the Ochotonidae (pikas). Although both descend from a common ancestor, their body sizes and geographic ranges diverged sharply, with pikas mostly occupying rocky, high-altitude habitats and leporids colonizing nearly every continent except Antarctica.⁴

Teeth Built for a Grassy World

One of the most striking evolutionary trends across herbivorous mammals over the past 20 million years has been the development of high-crowned teeth, a feature called hypsodonty. Rabbits are textbook examples. As grasslands spread during the Neogene, diets shifted toward fibrous, gritty plants that wear teeth down rapidly. Mammals with taller tooth crowns could survive longer on these abrasive diets, and in the drying landscapes of the late Miocene, only increasingly high-crowned mammals were able to expand their share of habitats and food resources.⁵

Rabbits took this a step further: their teeth grow continuously throughout life, an adaptation that compensates for constant wear from a diet of tough grasses and bark. This is not unique to lagomorphs, but it is fundamental to understanding how they thrive on vegetation that would grind down a fixed set of teeth within a few years. The link between open environments and high-crowned teeth is one of the clearest examples in paleontology of how climate and diet can drive anatomical change across entire groups of mammals.

A Digestive System for Low-Quality Food

Teeth are only half the story. Rabbits also evolved a highly specialized gut to extract nutrients from tough plant material. They are hindgut fermenters, meaning their large cecum (a pouch at the junction of the small and large intestines) does the heavy lifting of breaking down cellulose, rather than a multi-chambered stomach as in cows. Their digestive strategy revolves around high food intake and rapid intestinal transit, which lets them make good use of nutrient-poor diets.⁶

This system comes with a well-known quirk: cecotrophy. Rabbits produce two types of droppings. The first pass through the gut yields soft, nutrient-rich pellets (cecotropes) that the rabbit re-ingests directly from the anus, giving the gut a second shot at absorbing vitamins and microbial proteins. The hard, dry pellets you see on a lawn are the waste from the second pass. It is an unglamorous adaptation, but remarkably effective. Cecotrophy essentially turns a simple hindgut into a two-pass digestive system, extracting far more nutrition than would be possible otherwise.

The Iberian Cradle of the European Rabbit

When most people think “rabbit,” they are thinking of the European rabbit, Oryctolagus cuniculus, the ancestor of every domestic breed from the Flemish Giant to the Holland Lop. This species has a surprisingly narrow geographic origin. For most of its evolutionary history, Oryctolagus cuniculus was confined to the Iberian Peninsula (modern Spain and Portugal) and parts of southern France.

Genetic studies have identified two major mitochondrial DNA lineages within the species, called clades A and B, whose distributions map onto a northeastern and a southwestern Iberian refuge. After the last ice age, rabbits dispersed outward from both refugia: the southwestern populations moved north and northwest, while the northeastern ones spread south and west, eventually overlapping across a broad zone running from the southeast to the northwest of the peninsula.⁷ From Iberia, rabbits recolonized France as the climate warmed and Atlantic forests returned at the end of the last glacial period.⁸

It was only through human intervention, first by the Romans and later by medieval monks and traders, that European rabbits reached Britain, the rest of continental Europe, Australia, and eventually every inhabited continent. The species’ worldwide range today is almost entirely a product of the last two thousand years of deliberate introduction, not natural dispersal.

What Domestication Changed in the Brain

Rabbit domestication is thought to have gained momentum in medieval France, though the exact timing and whether there was a single domestication event remain debated. What is clearer is what happened inside the heads of the rabbits that were selected for tameness. Research comparing brain gene expression in wild and domestic European rabbits has found striking differences in two brain regions central to fear and memory processing.

In the amygdala, which processes threat signals, domestic rabbits showed significantly higher expression of genes tied to dopamine signaling. Every one of the twelve genes in that category was more active in domestic rabbits than in wild ones. In the hippocampus, domestic rabbits showed reduced expression of genes involved in a cellular structure called cilia. All 21 genes in that category were less active in the domestic animals.⁹ Dopamine is the brain’s reward and motivation chemical, so boosting its signaling could shift behavior away from constant fear toward curiosity and tolerance of human contact. The ciliary changes in the hippocampus are less intuitively obvious but may relate to how the brain processes spatial and environmental cues that trigger flight responses. Together, these findings suggest that tameness in rabbits was not just about selecting calm individuals but involved rewiring fundamental brain circuits.

Rabbits Versus Hares and Why the Difference Runs Deep

Rabbits and hares look similar enough that many people use the names interchangeably, but the two groups adopted quite different reproductive strategies early in their divergence. Hares are precocial: their young are born furred, open-eyed, and able to move within hours. Rabbits are altricial: their kits are born naked, blind, and completely helpless, tucked into fur-lined underground nests. This difference is not trivial; it shows up in skeletal anatomy. When researchers compared pelvic dimensions between a hare and a rabbit species while controlling for body size, the precocial hare had significantly larger pelvic dimensions in almost every measurement, consistent with the need to birth larger, more developed offspring.¹⁰

The altricial strategy lets rabbit mothers invest less energy per individual birth and instead produce larger litters more frequently, which can be a strong advantage in unpredictable environments where mortality is high. Hares, by contrast, produce fewer, more developed young that can outrun a predator almost immediately. Both strategies have been wildly successful: hares dominate open grasslands, tundra, and savannas, while rabbits have thrived in warrens across a broader range of habitats.

Blurred Boundaries Among Hares

If you think of species as neatly separated genetic units, hares will challenge that assumption. Genomic research has revealed that hybridization among hare species has been frequent, ancient, and ongoing. A comprehensive study of the hare radiation found recurrent introgression (gene flow between species) at every stage, from the deep origins of the genus to the present day. Ancient hybridization between northern hemisphere hare species has left a genetic legacy that includes shared variation in genes involved in circadian rhythm regulation, pigmentation, and thermoregulation, all traits that matter in highly seasonal environments.¹¹

Some cases are dramatic. In China, six hare species show evidence of frequent interspecific hybridization, and in one species, Lepus mandshuricus, the original mitochondrial DNA was completely replaced by mitochondrial DNA from two other species.¹² Similarly, the Iberian hare in its northern range carries extensive mitochondrial DNA from the mountain hare, an arctic species it replaced locally after the last ice age.¹³ These findings suggest that the evolutionary history of hares is less a neatly branching tree and more a tangled web, with gene swapping providing raw material for adaptation to new climates and habitats.

Seasonal Camouflage and Borrowed Genes

Several hare species that live in snowy environments molt from brown summer coats to white winter ones, a seasonal switch that keeps them camouflaged year-round. The molecular machinery behind this molt involves hundreds of genes orchestrated in waves. In the mountain hare, researchers identified over 600 differentially expressed genes during the autumn molt, with a major burst of gene activity early in the molt and a smaller pulse near the end. Genes involved in pigmentation, circadian rhythm, and even behavioral regulation all shifted their expression as the coat turned white.¹⁴

The regulation of this molt turns out to be surprisingly conserved: the mountain hare and the snowshoe hare, which are closely related but live on different continents, show significant overlap in which genes change expression during seasonal color change. But the story gets more interesting along the Pacific Northwest coast of North America, where some snowshoe hare populations stay brown in winter rather than turning white. Genetic work showed that this brown-in-winter trait arose through positive natural selection on a version of the Agouti pigmentation gene that originally came from black-tailed jackrabbits via ancient hybridization.¹⁵ In regions where snow cover is thin or patchy, a white coat in winter is a liability rather than an advantage, and borrowing an already-functional brown-winter allele from another species was faster than waiting for a new mutation to appear. This is one of the clearest demonstrations in mammals of adaptive introgression: evolution taking a shortcut by using genes acquired through interspecies mating.

Evolution You Can Watch in Real Time

Perhaps no example illustrates ongoing rabbit evolution more vividly than the arms race between wild European rabbits in Australia and the myxoma virus. When the virus was deliberately released in 1950 to control the continent’s enormous feral rabbit population, it killed over 99 percent of infected animals. What followed became a textbook case of host-pathogen coevolution. The virus evolved less lethal strains that kept rabbits alive long enough for mosquitoes to spread the infection more widely. Simultaneously, rabbits with even slight genetic resistance survived and reproduced. Short generation times and vast population sizes meant evolution could be tracked in real time.¹⁶

The pattern of resistance accumulation was not smooth. Rabbit resistance rose rapidly in the first decade, then plateaued for ten to fifteen years. A second sharp rise followed the introduction of European rabbit fleas in 1975, which created a new transmission route that exerted fresh selective pressure on both host and virus.¹⁷ And the virus did not simply settle into a comfortable middle ground. By the 1990s, viral isolates had evolved a new trick: instead of the classic myxomatosis symptoms, many strains now induced a lethal immune-collapse syndrome resembling septic shock, a phenotype not seen in the original virus or in strains from the 1950s.¹⁸ The virus, in effect, escalated the conflict rather than reaching a stable truce. This ongoing arms race remains one of the most detailed natural experiments in evolutionary biology.

Living Fossils on Island Edges

Not every rabbit lineage responded to environmental change by spreading and diversifying. The Amami rabbit, Pentalagus furnessi, survives only on two small islands in southern Japan and is one of the most evolutionarily distinct lagomorphs alive. It looks nothing like a typical rabbit: it has short ears, small eyes, stubby legs, and dark fur. It does not hop in the way continental rabbits do. Instead, its dense limb bones with thick walls and small inner cavities provide the skeletal robustness needed to navigate steep, rugged island terrain, a striking contrast to other lagomorphs that evolved lighter bones suited for leaping locomotion on open ground.¹⁹

The Amami rabbit is sometimes called a “living fossil,” though that term oversimplifies things. It retains features that other rabbit lineages discarded millions of years ago, but it has also adapted to its specific island environment in ways no ancient lagomorph needed to. Its bone histology reveals a slower life history than most rabbits, consistent with the reduced predation pressure and limited resources typical of island ecosystems. It is a reminder that evolution does not always mean becoming faster, bigger, or more widespread. Sometimes it means becoming perfectly suited to a tiny, specific place and then hanging on while the rest of the world changes around you.