Crocodiles play an important role within the ecosystem, use in tourism and trophy hunting. The Nile crocodile is the only crocodile in Namibia and little is known about its genetics and abundance. The Nile crocodile population has gone through a number of reduction events since 1957 and today the numbers of crocodiles is much reduced, but recovering. Small C. niloticus populations are under increased extinction pressure, because the genetic diversity of such populations can be low. A genetic diversity study has been performed on C. niloticus from the Okavango Delta in Botswana by Bishop and colleagues (2009). They found that the effective population ratio of this population was lower than expected while neutral genetic variation is still at moderate levels. The aim of our study is to determine whether the two populations in the river systems diverged due to geographical or other physical barriers to form distinct genetic populations with no recent gene flow expected.