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Background  Nile tilapia,  Oreochromis niloticus  (Linnaeus, 1758) is among the economically most important freshwater fish species in East Africa, and a major source of protein for local consumption. Human induced translocations of non-native stocks for aquaculture and fisheries have been found as a potential threat to the genetic diversity and integrity of local populations. In the present study, we investigate the genetic structure of  O. niloticus  from 16 waterbodies across Ethiopia using 37 microsatellite loci with SSR-GBAS techniques.    Results  The samples are structured into three main clusters shaped either by biogeographic factors or stocking activities. High  F   ST   values (Global  F   ST   = 0.438) between populations indicate a high level of genetic differentiation and may suggest long term isolation even within the same drainage systems. Natural populations of the Omo-Turkana system and the lakes in the Southern Main Ethiopian Rift showed the highest genetic variability while low variability was found in stocked populations of lakes Hora, Hashenge and Hayq.    Conclusions  The results presented herein, may provide an essential basis for the management and conservation of the unique genetic resources in northern East Africa, and advance our understanding of biodiversity, phylogeny, evolution and development towards phylogenetically more accurate taxonomic classifications.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12862-021-01829-2.

bmc ecology and evolution

Genetic diversity of Nile tilapia (Oreochromis niloticus) populations in Ethiopia: insights from nuclear DNA microsatellites and implications for conservation