What Animals Have Hemipenes? And Why They Have Two

Hemipenes are the paired copulatory organs found in squamates, the reptile group that includes all lizards and snakes. Unlike the single penis seen in mammals, birds that have one, and crocodilians, squamates carry two separate intromittent organs tucked inside the base of the tail, one on each side of the cloaca. The reason they come in pairs traces back to an unusual quirk of embryonic development, and the way males actually use them in the wild turns out to be stranger and more strategic than simple anatomy would suggest.

Which Animals Actually Have Hemipenes

The short list is squamates and only squamates. That means every species of snake, lizard, amphisbaenian (the burrowing “worm lizards”), and tuatara-adjacent legless lizard you can think of belongs to a group whose males have hemipenes. With roughly 11,000 recognized squamate species, that covers an enormous range of body plans, from tiny leaf chameleons to reticulated pythons. In all of them, the hemipenes extend from the lateral edges of the cloaca rather than protruding from a single midline structure the way a mammalian penis does.¹

Other reptile groups do not share this arrangement. Crocodilians and turtles have a single penis, and most birds lack an external intromittent organ altogether (the few that have one, like ducks and ostriches, also have a single structure). Mammals are uniformly single-penised. The hemipenis is a squamate invention, and understanding why requires looking at how these organs form in the embryo.

Why They Come in Pairs

The answer lies in where the tissue comes from during development. In mammals, the genital tubercle that becomes the penis or clitoris grows from tissue on the front side of the cloaca. Paired swellings appear early on but quickly fuse at the midline into a single structure. In squamates, something fundamentally different happens: the genital tissue buds off from the same cell populations that form the hindlimbs.² Because hindlimbs are inherently paired, the genitalia that develop from them are paired too.

Cell-tracing experiments in embryos showed that the tissue contributing to squamate genitalia originates from a strip of lateral plate mesoderm running from the back edge of the developing hindlimb bud to the front of the tail bud.³ This is essentially the same zone that gives rise to limb tissue. In mammals and birds, the cloaca sits in a different relative position, so the genital-organizing signals recruit tail bud cells instead of limb cells, producing a single midline organ. The shift in cloacal position across evolutionary time is what split genital development down two different paths: one that yields a single penis, and one that yields a pair of hemipenes.

This means having two hemipenes is not an adaptation that evolved because two was better than one. It is a structural consequence of the developmental program squamates inherited. The paired organs are, in a sense, a leftover signature of their limb-building machinery. What is adaptive is how squamates have exploited the situation once they had two organs to work with.

How Males Use the Two Sides

Only one hemipenis is inserted during any single mating event. Males evert one organ from its resting position inside the tail base, and it inflates with blood and lymph to become functional. After mating, it retracts. The interesting part is what happens at the next mating. In multiple species, males show a strong tendency to alternate which hemipenis they use from one copulation to the next.

In brown anole lizards mated daily with different females, males significantly favored switching sides between successive copulations. This alternation pattern held when matings were spaced up to about three hours apart and was still detectable after a full day, though it faded after roughly three days.⁴ The pattern depends on actual intromission occurring, not just mounting. When researchers forced males to use a specific hemipenis, the alternation reset, suggesting that sensory feedback from insertion itself drives the switching.⁵

Garter snakes show the same tendency. In that species, researchers proposed that alternation lets the unused hemipenis replenish its supply of copulatory plug material, a gelatinous substance males deposit in the female’s cloaca after mating to block rival males’ sperm.⁶ If a male mates twice in quick succession using the same side, he risks delivering a smaller, less effective plug the second time. By switching to the fresh hemipenis, he gets a full plug and a fresh sperm payload. In species where females mate with multiple males in rapid succession, this biological reload could be the difference between siring offspring and being outcompeted.

Spines, Hooks, and the Role of Sexual Selection

Hemipenes are not simple tubes. Their surfaces can be covered with spines, hooks, ridges, calyces (cup-shaped structures), and fleshy lobes, and the specific ornamentation varies wildly between species. A study examining hemipenis morphology across fifteen snake species from four families found ornamentation patterns ranging from large basal spines to elaborate crenulated folds, and concluded that sexual selection is the primary force driving this diversity.⁷ Some ornate morphologies appear designed to lock the hemipenis inside the female during copulation, while others seem tied to the variety of mating behaviors observed across species.

The spines are not merely decorative. In red-sided garter snakes, researchers surgically removed the large basal spine from the hemipenis and found that males could still mate, but copulation was much shorter and the copulatory plugs they deposited were smaller than those of intact males.⁸ That spine physically anchors the hemipenis during copulation and helps with the transfer of both sperm and the plug itself.⁹ Without it, the male is at a reproductive disadvantage: shorter copulation gives less time to deliver sperm, and a smaller plug is easier for a rival male to dislodge.

This creates something of an arms race. Males evolve more elaborate or effective locking structures, while females may evolve genital morphology that either accommodates or resists those structures, depending on whether longer copulation benefits them. Research on a South American lizard species found that male and female genital traits scale together as body size increases, a pattern consistent with coevolution between the two sexes’ reproductive anatomy.¹⁰ The genitalia of squamates are not just plumbing; they are an active theater of sexual conflict and cooperation.

Females Have a Paired Counterpart

For a long time, the female equivalent of hemipenes was either ignored or assumed not to exist. That changed with the discovery and formal documentation of hemiclitores in female snakes and lizards. The first confirmed evidence of hemiclitores in snakes came from dissections of female death adders, which revealed paired structures containing extensive erectile tissue with blood-filled vascular spaces and dense nerve bundles.¹¹ The presence of blood-filled erectile tissue suggests these organs can engorge, and the abundant nerve bundles suggest they provide sensory feedback during mating.

In lizards, hemiclitores had been noted earlier, and their structure broadly mirrors the hemipenis in miniature: they share the same basic layout of an apex, sulcus, and basal region, along with paired retractor muscles. But there are differences. The hemiclitoris lacks the cartilage found in hemipenes, has thinner surface tissue, and is typically smaller.¹² These structures were overlooked for decades partly because researchers historically focused on male anatomy for species identification purposes, and partly because the hemiclitores are small enough to be mistaken for other tissue during dissection.

The existence of hemiclitores also makes developmental sense. Both male and female squamate embryos initially develop hemipenes from the same tissue. In females, these structures shrink and largely regress before hatching, but they do not disappear entirely. The hemiclitores are what remains, and their nerve-rich, erectile composition suggests they are functional organs, not vestigial leftovers.

How Embryos Build and Sometimes Lose Hemipenes

The hormonal choreography behind hemipenis development is surprisingly well studied in anole lizards. Both sexes begin forming hemipenes during embryonic life, but in females the structures regress before the animal hatches.¹³ This regression is driven by estrogen: when researchers treated embryonic eggs with estradiol, hemipenes and their associated muscles were absent in the resulting hatchlings regardless of genetic sex. Androgens had the opposite effect. Treating female embryos with testosterone or its derivative rescued their hemipenes, preventing regression and even causing the organs to enlarge and evert.¹⁴

What this tells us is that the default embryonic program builds a set of hemipenes in every squamate, and it takes active hormonal signaling to suppress them in females. The molecular toolkit is shared; only the hormonal environment differs. This shared starting point explains why female hemiclitores resemble small hemipenes so closely, and why occasional intersex animals are found in wild populations with partially developed organs on one or both sides.

Why Hemipenis Shape Matters for Identifying Species

Taxonomists have used hemipenis morphology to classify squamates for well over a century, and in many groups it remains one of the most reliable tools for distinguishing closely related species. Two snake species that look nearly identical in scale counts and body proportions may have hemipenes with completely different ornamentation patterns. The logic is straightforward: because hemipenis shape evolves under intense sexual selection pressure, it diverges rapidly between lineages, making it an unusually informative character for species-level identification.

That said, the field acknowledges a gap. Hemipenes have been described in great detail for many snake and lizard families, but there have been few attempts to trace how these structures changed across the evolutionary transition from lizards to snakes, or to reconstruct ancestral hemipenis morphology for major squamate clades.¹⁵ Part of the difficulty is that hemipenes are soft tissue and do not fossilize, so the evolutionary story has to be pieced together entirely from living species. Another challenge is that the same ornamental feature, like a forked tip or a calyculate surface, can evolve independently in unrelated groups, complicating efforts to build family trees based on genital shape alone.

When Hemipenes Cause Medical Problems

For anyone who keeps snakes or lizards in captivity, hemipenis prolapse is one of the more common reproductive emergencies. A prolapsed hemipenis is one that has everted and cannot retract, either because of infection, swelling, trauma, or substrate material wrapping around it. In mild cases, veterinarians can manually reduce the prolapse by cleaning the tissue and gently pushing it back into the tail base. When the tissue is too damaged or necrotic to save, the hemipenis can be surgically removed. Because hemipenes are not connected to the urinary tract in the way a mammalian penis is, amputation of one or even both hemipenes does not affect a reptile’s ability to excrete waste.¹⁶ A male that loses one hemipenis still has the other for mating; a male that loses both can urinate normally but can no longer breed.

Prolapse is more common in captive reptiles than in wild ones, likely because captive conditions sometimes promote repeated mating attempts, obesity, or bacterial infections that increase the risk. Keepers who notice an everted hemipenis that does not retract within a reasonable window should treat it as an urgent veterinary matter, since exposed tissue dries and becomes necrotic quickly. The fact that hemipenis removal is a survivable, relatively low-risk surgery is a practical consequence of the organ’s anatomy: it is a separate, self-contained structure with its own blood supply and musculature, not a shared duct for waste and reproduction.

Asymmetry and Handedness

Not all hemipenes are created equal within a single animal. In some species, the right hemipenis is consistently larger than the left, or vice versa. Garter snake males, for example, tend to have size asymmetries between their two hemipenes.⁶ Whether this produces a behavioral preference for one side, a kind of reptilian handedness, is a question researchers have poked at but not fully resolved. The alternation tendency appears to override any size-based preference in species where it has been tested, suggesting that the reload advantage of switching sides matters more than using the bigger organ every time.

In lizards, the tail base where hemipenes are stored can be visibly wider in males than in females of the same species, which field biologists sometimes use as a quick way to sex an animal without invasive probing. The hemipenes essentially bulk out the tail base, giving males a slightly swollen appearance at the vent that experienced herpetologists can spot at a glance. This external cue is less reliable in species with very small hemipenes or very thick tail bases, but in many common pet species like leopard geckos and ball pythons, it is a useful first-pass sexing method.