Amniote external genitalia vary significantly in form. Most amniote species have a single phallus, although some have paired hemiphalluses and others lack a phallus altogether. Intromittent amniote phalluses have either an open urethral groove or a closed urethral tube. This considerable degree of morphological variation has confounded our understanding of phallus evolution. To ask whether differences in adult phallus anatomy reflect distinct developmental and evolutionary origins, we compared external genital development in three reptiles with distinct external genital anatomies: the American alligator has a single phallus, the green anole has paired hemiphalluses, and the tuatara lacks a phallus. We find that in the alligator, anole, and tuatara, early stages of cloacal and external genital patterning include the formation of genital protuberances adjacent to the cloaca and developing hindlimbs. In the alligator, the genital tubercle, or embryonic penis and clitoris, forms from outgrowth of genital mesenchyme beneath the ventral body wall, adjacent to the cloacal membrane and medial to the hindlimb buds. The anole hemiphalluses initiate as genital buds at the ventral base of the hindlimb buds, yet these buds remain separate and mature into two distinct hemipenes in males and hemiclitores in females. Histological analysis shows that, despite absence of an adult phallus, tuatara embryos develop paired genital eminences adjacent to the cloaca. Conservation in the events comprising early external genital development across amniotes supports the hypothesis that external genital anlagen are a shared, derived character of Amniota, and subsequent divergence in morphogenesis generates the variation observed in adult phallus morphology.