Fragmentation affects population structure and tree diversity. However, the main causes of fragmentation and their consequences on population structure are still unclear. This study evaluated some causes of gallery forest (GFs) fragmentation and their effect on Pentadesma butyracea population structures in Benin. Twelve P. butyracea GFs were selected in semi-arid and sub-humid ecological zones. Populations were identified varying fragmentation indicators (gallery width, distance to the nearest population, current area, shape of GFs and rate of area loss during the last three decades) to assess the species diversity, tree densities and shape of diameter class distribution (SDCD) of trees. Generalized linear regression was used to test the effect of fragmentation on species diversity, density and SDCD. The proximity of villages, farms to GFs increased fruit harvest rate and GFs area reduction. Interaction between gallery width, area loss rate and ecological zone had a significant effect on species diversity, density and marginally on SDCD. The results are valuable in the perspective that they showed the importance of the combined effect of habitat fragmentation and provide a better understanding of the actions to be considered for sustainable conservation of GFs and P. butyracea trees.