The cladogram below follows the topology from a 2012 analysis of morphological traits by Christopher A. Brochu and Glenn W. Storrs. Many extinct species of Crocodylus might represent different genera. C. suchus was not included, because its morphological codings were identical to these of C. niloticus. However, the authors suggested that it could be explained by their specimen sampling, and considered the two species to be distinct.
Crocodylus species originated from an ancestor in the Indo-Pacific region between and . They radiated into Africa between and . This was followed between to by a trans-Atlantic migration to the Americas.