Despite their high abundance and species richness, tilapiines have been compromised by various factors especially overfishing, climate change, and un-controlled fish translocations. Fish translocations have negatively impacted native tilapiine populations through competition, predation, hybridization, and introgression compromising their genetic integrity. The hybridization levels of different tilapiines in the Lake Victoria basin remains an understudied aspect relatively. The study utilized nuclear microsatellite and mitochondrial DNA (mtDNA ) genetic markers to investigate hybridization signals and compare the genetic diversity of different tilapiines in Lake Victoria, Kenya, using next-generation sequencing. Low levels of hybridization from Oreochromis niloticus into other Oreochromis species were detected by Bayesian clustering analysis and principal coordinate analysis (PCoA ). The results contribute to the need for conservation measures of these fish species.