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ABSTRACT Despite the remarkable morphological diversity found in vertebrate genitalia, it has historically been difficult to quantify shape variation of soft tissue structures due to limitations of 3D landmarking methods. New techniques such as automatic landmarking now allow us to examine such structures in detail, and with these methods we quantify the intraspecific variation in the genitalia of Burmese pythons (Python bivittatus). Despite previous assertions that a vaginal pouch is not present in pythons, we find thatP. bivittatushave well developed vaginal pouches, that are morphologically diverse, and change shape over ontogeny. Vaginal pouches and hemipenes are isometric. Hemipenes also vary in shape ontogenetically, but we find no evidence of directional asymmetry in shape or size between adult right and left hemipenes suggesting a lack of laterality. We identify a potentially intersex neonate with hemipenes, testes, and a vaginal pouch. We discuss our results in the context of snake genital evolution and suggest other mechanisms for selection beyond the standard “lock and key” hypothesis. Future work examining genital shape variation of other snake families will provide more insight into the coevolutionary patterns shaping the genitalia diversity across snakes and vertebrates more broadly.