Anthropogenic disturbances, such as illegal harvesting and livestock browsing, often affect natural forests. However, the resulting tree species diversity, composition, and population structure have rarely been quantified. We assessed tree species diversity and importance value indices and, in particular, Balanites aegyptiaca (L.) Del. population structure, across 100 sample plots of 25 m × 40 m in disturbed and non-disturbed sites at the Dinder Biosphere Reserve, Sudan, from April 2019 to April 2020. We found that the tree species diversity in non-disturbed sites was more than double that of disturbed sites (p < 0.001, T = 32.6), and seedlings and saplings comprised more than 72% of the entire tree population (F2,48 = 116.4, p = 0.034; F2,48 = 163.2, p = 0.021, respectively). The tree density of B. aegyptiaca in the disturbed site was less than half that of the non-disturbed site (p = 0.018, T = 2.6). Balanites aegyptiaca was seven times more aggregated in disturbed sites compared to more regularly spaced trees in non-disturbed sites (T = 39.3 and p < 0.001). The poor B. aegyptiaca population status of the disturbed site shows that the conservation of this vulnerable species is essential for a sustainable management and utilization scheme.