Genetic divergence of baobab (Adansonia digitata) in the North East and West of Nigeria was investigated. The seeds collected from 36 populations of Adansonia digitata were thoroughly washed from the pulp, dried and sown in polyethylene pots and arranged in completely randomized design (CRD) with three replications in the nursery of Savanna Forestry Research Institute of Nigeria, (FRIN), Zaria Station. The leaves of the seedlings were assessed at 16 weeks after sowing (WAS) for nutritional traits such as carbohydrate, crude protein, fat, moisture content, fiber and ash. Highly significant differences were observed in all the traits assessed showing that high variability exists among the populations. Mean separation and comparisons were also consistent with the observed variability in all the traits of the genotypes in the 36 populations. Mahalanobis D² statistic and wards minimum variance grouped the 36 populations into four clusters: I (25), II (3), III (7) and IV (1). Clusters IV and I had the highest inter-clusters value and intra-cluster distance. Clusters II and I had the least values of D 2 and D 2 of the inter cluster and intra cluster distance. Furthermore, cluster I had the highest population (25) and cluster IV was observed to be an isolated cluster with only one population and 0 intra-cluster values. Crosses can be made among the genetically divergent populations of baobab to develop genotypes for higher nutritional quality in the leaves as well as withstand both biotic and abiotic stress arising from the environment.