The Nile crocodile has experienced numerous stages of illegal hunting pressures in the mid-20thcentury
across most of the species’ distribution. The reduced Nile crocodile populations have shown
partial recovery and it is currently considered as a “lower risk” / “least concern” species on the Red List
of International Union for Conservation of Nature. In Namibia, however, the Nile crocodile is recognised
as a protected game species under the Nature Conservation Ordinance No 4 of 1975, allowing trophy
hunting of the species only with the issuing of a hunting licence. Census and genetic data of the Nile
crocodile is limited or non-existing in Namibia and the country has recently developed a species
management plan to conserve the wild populations. During 2012 an aerial survey was conducted along
the Lower Kunene River to estimate the abundance and distribution of the Nile crocodile population, by
the use of a recently developed N-mixture model. Within the Lower Kunene River system a direct count
revealed 562 crocodiles regardless of size, and an estimated population size of 806 individuals, after bias
correction. The analyses suggested the class-structured model produced unbiased estimates of the Nile
crocodile population in the Lower Kunene River system. To contribute to the conservation efforts of the
Nile crocodile in the Lower Kunene River, the study also assessed the genetic diversity and structure
within the Kunene and Okavango River system in comparison to neighbouring river basins. This study
aimed to develop molecular markers, to assess the patterns of genetic diversity and population structure
generated from 11 Short Tandem Repeats and the mitochondrial DNA, control region. The Lower
Kunene and Okavango populations indicated a recent divergence with a single haplotype shared among
the 64 samples sequenced and interestingly the haplotype was shared with populations in Gabon and
Uganda. Moreover, there was no sharing of haplotypes found between the Lower Kunene and Okavango
and the Lower Shire River system. Estimated for pairwise population differentiation, F-statistics,
AMOVA and factorial correspondence analysis (FCA), based on Short Tandem Repeats, indicated
significant structuring among the populations. Additionally, Bayesian clustering analyses detected three
putative ancestral gene pools, of which two were present in the Okavango River population, supporting
the findings of the Nile crocodile to be structure according to river basin formation. Despite no expansion
or population bottleneck detected in the Nile crocodile populations, a contemporary genetic bottleneck
may have gone undetected due to the crocodile’s long-life span and breeding between overlapping
generations. The contemporary restriction of gene flow and historical river topography are the most likely
cause of genetic structure in the Nile crocodile populations of today. Even though the Kunene and
Okavango Nile crocodile populations are experiencing different environmental and evolutionary
pressures, the genetic data suggest a single evolutionary significant unit, with two management units. The
Okavango River had a broad sampling range for the study, however both river populations will require
more samples to validate fine-scale genetic structure.