Background and Objective: In Nigeria, there is a paucity of information on the genetic similarity among wild Oreochromis niloticus species. Though there are assertions based on morphological observation, by fish farmers and some researchers of fisheries that most of these species in the wild are no longer pure and possibly hybridizing. Most molecular assessments are usually among tilapia species with limited sample coverage of O. niloticus species or of a lower marker. This was a preliminary investigation of the genetic similarity of Oreochromis niloticus from selected water bodies along the River Niger, in six states of Nigeria, using SSR markers. Materials and Methods: Similarity levels among Oreochromis niloticus from water bodies in six states in Nigeria were assessed using seven SSR markers with their various primers (UNH 208, 143, 104, 022, 119, 180 and 156), which were selected from the NCBI database. Only UNH 104, UNH143 and UNH 022 produced DNA amplifications. Phylogenetic representation using UPGMA cluster analysis produced a dendrogram with a total of 118 clusters grouped into 7 major clusters with up to 8 subgroups, indicating different degrees of variation and similarities. Results: Genetic similarities were observed at various coefficient levels, possibly due to hybridization. At the coefficient level of 1 or 100%, 39 clusters occurred with different samples on each cluster indicating they are genetically the same. Samples from South Delta (SSD), South West Oyo (SWO) and North West Kebbi (NWK) states were always present in each cluster at this coefficient level. A lot of migration is likely taking place among these fishes. The seven major clusters A, B, C, D, E, F and G at varying degrees of similarity 73, 67, 64, 59, 56, 48 and 44% showed the decreasing order of genetic similarity. Conclusion: These data supported the view that the very high similarity between tilapia from these water bodies stems from its highly prolific nature which may have led to a high probability of hybridization between species and strains. The genetic distance between strains may suggest that there are varying levels of genetic variability among O. niloticus in Nigeria water bodies under study.