Abstract The present study describes the location and nuclear organization of the serotonergic system in a representative of the order Crocodylia, the Nile crocodile ( Crocodylus niloticus). We found evidence for serotonergic neurons in three regions of the brain, including the diencephalon, rostral and caudal brainstem, as previously reported in several other species of reptile. Within the diencephalon we found neurons in the periventricular organ of the hypothalamus, but not in the infundibular recess as noted in some other reptilian species. In addition we found serotonergic neurons in the pretectal nucleus, this being the first description of these neurons in any species. Within the rostral brainstem we found medial and lateral divisions of the superior raphe nucleus and a widely dispersed group of neurons in the tegmentum, the superior reticular nucleus. In the caudal brainstem we observed the inferior raphe nucleus and the inferior reticular nucleus. While much of the serotonergic system of the Nile crocodile is similar to that seen in other reptiles the entire suite of features appears to distinguish the crocodile studied from the members of the Squamate (lizards and snakes) and Testudine (turtles, tortoises and terrapins) reptiles previously studied. The observations are suggestive of order-specific patterns of nuclear organization of this system in the reptiles, reflecting potential evolutionary constraints in the mutability of the nuclear organization as seen for similar systems in mammals.