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Tilapia aquaculture farming expansion in rift valley region has led to transfer of different Oreochromis species from fish ponds to natural ecosystems such as river and lakes. This has led to the dwindling in numbers as well as compromising the genetic integrity of the native species through competition, hybridization and introgression. Introductions of tilapia into Lake Baringo from unverified sources and unknown species has been reported in the past but has continued due to rapid expansion of tilapia farming. The study aimed at evaluating the current genetic diversity of Oreochromis species in Lake Baringo in order to determine the recent species introductions and effects on endemic populations of the Nile tilapia Oreochromis niloticus baringoensis. Morphological and molecular techniques involving mtDNA markers (Cytochrome Oxidase 1, Control region and D-loop genes) were used to identify tilapia species from the lake. The observed morphometric and meristic differences showed variations congruent with two tilapia species Oreochromis niloticus and Oreochromis spirulus. Genetic studies revealed four haplotypes based on maximum likelihood phylogenetic trees on mtDNA Cytochrome Oxidase 1 and seven haplotypes each for mtDNA Control region and D-loop marker genes. The haplotypes were identified as O. n. baringoensis, O. spilurus, O. n. vulcani, O. niloticus (unknown) and the hybrids of O. n. baringoensis with O. leucostictus. These findings confirm indications that increased aquaculture activities around Lake Baringo basin have led to continued species introduction and hybridization in the main lake, thus endangering the native species O.n baringoensis which form an important role in commercial fisheries for the communities around the lake.