Abstract: Background and Objective: Improvement and conservation strategies of animal genetic resources require first of all, a full knowledge of breeds’ diversity and genetic structure. In order to disclose the current genetic structure of Senegalese local cattle breeds, this study has used the population genetics approaches. Materials and Methods: The DNA samples were taken from 120 unrelated cattle animals sampled from the main livestock breeding areas in Senegal. Genotyping was carried out using 11 microsatellite loci selected within the panel recommended by ISAG-FAO for cattle breeds’ genetic characterization. Genetic differentiation and structure analysis were performed using bioinformatics’ softwares. Results: The FST, measure of population differentiation indicated a mean value of 0.047±0.011, (p<0.05), followed with a mean gene flow (Nm) of 5.06. The Bayesian analysis indicated three clusters. The first one grouped mainly the N’Dama cattle, the second the majority of Djakore “hybrid” population and the last one clustered the zebu’s populations. Conclusion: Population structure analysis has revealed at present that Senegalese local cattle breeds were not running towards genetic erosion, nevertheless they deserve to be closely monitored to avoid the disappearance of important adaptive traits.