The Nile crocodile (Crocodylus niloticus) is an ancient icon of both cultural and scientific interest. The species is emblematic of the great civilizations of the Nile River valley and serves as a model for international wildlife conservation. Despite its familiarity, a centuries-long dispute over the taxonomic status of the Nile crocodile remains unresolved. This dispute not only confounds our understanding of the origins and biogeography of the 'true crocodiles' of the crown genus Crocodylus, but also complicates conservation and management of this commercially valuable species. We have taken a total evidence approach involving phylogenetic analysis of mitochondrial and nuclear markers, as well as karyotype analysis of chromosome number and structure, to assess the monophyletic status of the Nile crocodile. Samples were collected from throughout Africa, covering all major bioregions. We also utilized specimens from museum collections, including mummified crocodiles from the ancient Egyptian temples at Thebes and the Grottes de Samoun, to reconstruct the genetic profiles of extirpated populations. Our analyses reveal a cryptic evolutionary lineage within the Nile crocodile that elucidates the biogeographic history of the genus and clarifies long-standing arguments over the species' taxonomic identity and conservation status. An examination of crocodile mummy haplotypes indicates that the cryptic lineage corresponds to an earlier description of C. suchus and suggests that both African Crocodylus lineages historically inhabited the Nile River. Recent survey efforts indicate that C. suchus is declining or extirpated throughout much of its distribution. Without proper recognition of this cryptic species, current sustainable use-based management policies for the Nile crocodile may do more harm than good.

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Conservation and management of widespread species can be improved if populations exhibiting genetic differentiation are recognized as local management units. Specimens of Nile crocodile (Crocodylus niloticus) corresponding to major river drainage systems from Eastern Africa and Madagascar, and a small set of samples from Western Africa, were analyzed using multilocus genotyping to evaluate the potential to discriminate among locations and to assign individuals to population of origin. Populations from all sampled regions exhibited marked levels of genetic and genotypic differentiation as assessed by significant F ST values and Bayesian analysis of population structure. At the regional level, the majority (94%) of all specimens were successfully assigned to the population of origin using only four microsatellite loci. Three populations sampled within Madagascar required the use of 12 loci for successful assignment of greater than 84%. Our findings demonstrate a need for alternative management strategies that consider the biogeographic sub-structuring of Nile crocodiles associated with major river drainages in Africa and Madagascar.