Maize is attacked by many post-harvest pests including Sitophilus spp and Prostephanus spp, which causes remarkable loss during storage. Approximately 30 to 40 % loss in the absence of treatment has been reported worldwide. This study compare genetically Central African and Senegalese populations of Sitophilus zeamais from various agroecological zones using 3 markers namely cytochrome b, cytochrome oxidase and nuclear 28S gene. S. zeamais samples were analyzed on both of two other sites 34 for the 28S gene; 68 for cytochrome b and 36 for the cytochrome oxydase. Results analyzed by AMOVA have shown high genetic variation outside population of each country (6.17 % with Cyt b; 21.45 % with 49.83 % and COI in the case of 28S) and low within subpopulations (-10.06 % for Cyt b, 9.36 % for the COI and-15.23 % for 28S). Majority haplotype is shared between the two populations for 28S and cytochrome b genes and there is a very high haplotype diversity in populations of Senegal considering the Cytochrome b gene (0.781 + /-0.00364) while with COI and 28S, high values of diversity are observed in Central African sequences, respectively 1.000 + /-0.00274 and 0.867 + /-0.011. Genetic differentiation obtained according to the geographical origin is significant between the two populations; however, it is not at the level of subpopulations. Developed by the three approaches (parsimony, likelihood and Bayesian) phylogenetic trees are resolved and show a speciation of the two populations according to the geographical origin.