Previous investigations of genetic diversity across the distribution of the Nile crocodile (Crocodylus niloticus) confirmed the existence of two genetically distinct species of true crocodile (genus Crocodylus) in Africa. These taxa correspond roughly to an eastern/southern African species (Crocodylus niloticus) and a central/western African species (Crocodylus suchus). Analysis of historical museum specimens demonstrated that both species existed concurrently in the Sudanese Nile until the early 20th century and genetic analyses of historical museum specimens of mummified crocodile hatchlings from Egyptian tombs located along Egyptian Nile were found to be C. suchus.

Here we present the first assessment of mitogenomic data from an adult Egyptian crocodile mummy from a center of crocodile worship and identify this specimen as C. suchus. Our data suggest that C. suchus was selectively chosen for mummification and support an accurate Egyptian cultural taxonomy as described by Herodotus in the fourth century BC and used by Etienne Geoffroy Saint-Hilaire to describe Crocodylus suchus in 1807. Crocodylus suchus has experienced a range contraction possibly due to climate change and the drying of the Sahara over the recent past. Our data identifying an adult crocodile mummy as C. suchus might indicate the historical natural presence of this species in the Egyptian Nile along with C. niloticus. Additional samples of crocodiles from both bioarchaeological and paleontological contexts will be required to confirm this.