Nile perch (Lates spp.) was introduced into Lake Victoria only five decades ago but is now well established and distributed throughout the lake. Given the extensive size of the lake, there is a possibility of isolation by distance that can lead to local adaptations. Microsatellite DNA variability was used to assess the genetic diversity and to define the population structure of Nile perch collected from 22 different geographical locations within Lake Victoria. In total, 432 individuals were genotyped at nine microsatellite loci. Analyses of multilocus microsatellite genotypes revealed that genetic diversity of Nile perch of Lake Victoria is relatively high (H_E = 0.68). Results also reveal shallow but significant genetic differentiation (F_ST = 0.029, P < 0.05). STRUCTURE indicated that Nile perch of Lake Victoria was made up of two (K = 2) genetically distinct populations. Separate analysis for each of the two groups also revealed relatively high genetic diversity for each group (H_E[N1] = 0.73 and H_E[N2] = 0.64). These results are surprising given that Nile perch was only recently introduced and is known to be migratory by nature. We interpret these results in light of multiple introductions from two different source populations of Nile perch and discuss implications of these results for the region's fisheries management.