This study evaluated the spatial genetic structure of baobab (Adansonia digitata L.) populations from three agroecological sites located in sahelian zone of Senegal using ITS1, 5.8S rDNA and ITS2 gene sequences. To determine the extent of isolation, gene sequences were analyzed between and among three sahelian baobab populations. At least 25 haplotypes of baobab (A. digitata L.) were revealed in Senegal (6, 9 and 10, respectively in Dakar, Bandia and Widou Thiengoly). Private haplotypes found in each locality show that there is an adaptation of the plant to environmental conditions prevailing in each site. Indeed, nucleotide diversity was more important in Dakar (0.00527); it ranges from 0.00483 to 0.00060 for Bandia and Widou populations, respectively. Curves of mismatch distribution show that the population of Ferlo has undergone a recent demographic expansion. Although Bandia and Dakar populations were polyphyletic; each shows a balanced expansion. Fst values ranging from 0.62946 to 0.90712 correlates a strong genetic differentiation between sites. A correlation between geographic and genetic distances was not highlighted by the Mantel's test but phylogenetic trees of maximum likelihood and Bayesian inference have assigned two clades demonstrating that population of Ferlo (Widou) form a different ecotype from those of Bandia and Dakar.