The baobab tree (Adansonia digitata L.) is a key indigenous fruit species of semi-arid sub-Saharan Africa, valued for its nutritional, economic, and ecological importance. While considerable information exists for its ecology and genetic diversity in Western and Southern Africa, Eastern Africa—particularly Sudan—remains understudied. Sudan hosts the northernmost populations of baobab, which may possess unique adaptations to arid conditions, yet these populations face increasing threats from habitat loss, climate change, and anthropogenic pressures. This study investigated morphological and genetic diversity among 306 baobab trees across seven locations in the Nuba Mountains, South Kordofan, Sudan. Morphological traits, including diameter at breast height, tree height, and fruit characteristics, were assessed alongside genetic diversity using microsatellite markers. Significant variation (P<0.05) in dendrometric traits was observed, with the southeastern region displaying the largest trees, while fruit morphology showed limited differentiation. Genetic analysis using Bayesian clustering revealed two distinct groups: one comprising mostly individuals from the southwestern site and another encompassing the remaining populations. Notably, the southwestern population exhibited the highest genetic diversity. Trees located near homesteads showed slightly elevated genetic diversity, suggesting historical patterns of human-mediated admixture, although no clear environmental gradient was associated with fruit morphometrics. These findings highlight the influence of human settlement on genetic structure and emphasize the need for targeted conservation strategies. Further localized studies are essential for the development of effective in situ and ex situ conservation measures to preserve baobab genetic resources in Sudan's marginal environments.