The present study is part of an aquaculture developmental program held in Burkina Faso. The final aim is to generate a genetic selection program for an Oreochromis niloticus strain presenting good performances in both growth and reproduction. A characterization of the genetic diversity within and between wild and domestic populations was performed using Restricted Fragment Length Polymorphism (RFLP) of the mitochondrial DNA (mtDNA). Muscle or fins were sampled from 142 individuals in 7 different sites on the 3 main hydro-graphic basins of Burkina Faso (Comoé, Volta and Niger). DNA was extracted using a commercial kit (Promega). The fragment Nd-5/6 (2 500 bp) of mtDNA was amplified by PCR using primers C-GLU and C-LEU3. The amplified products were then digested using one of the six following restriction enzymes: AluI, HaeIII, HinfI, HpaII, RsaI, and Taq I. Haplotype frequencies of the mtDNA per population were calculated from the mtDNA data. When using TaqI, we obtained 4 haplotypes in the basin of Comoé, 3 in that of Volta and only one in the basin of Niger. While the haplotype B is fixed in the Niger basin and the haplotype C dominants in the Comoé basin, haplotype A is only found in the Volta basin. Within the Volta basin, we observed differences in the C haplotype frequencies when we compared the domesticated Bazèga population with the wild population of Bama. The populations of Bazèga could have been introgressed by those coming from Kompienga as the frequency of haplotype C is higher in the Kompienga population, also visible in the Bazèga population. It appears that some individuals of Kompienga population are also maintained in the same rearing station of Bazèga. This distribution revealed heterogeneity of the Oreochromis niloticus populations of Burkina Faso. A larger number of individuals are being analysed presently with Taq I in order to validate these results. Further studies will consider the possible association of these genetic population differences,