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Indigenous woody species are important natural resources in West African savannas. Information about their population structures and response to human impact, particularly land use, however, is scarce. In this study, we explored (1) the effect of land use on the population structure of woody savanna species; and (2) searched for species with similar population structures related to comparable ecological preferences. Using generalized linear models, we separately analyzed the size-class distribution (SCD) of 30 species to reveal the influence of three land cover types (non-arable land, fallows, and protected areas) on population structures. Generalized linear models were applied to identify comparable population structures of species with similar ecological preferences. We were able to identify five groups for shrub species and four groups for tree species with different population structures and comparable ecological preferences. In terms of human impact, we detected four groups of species responding similarly to land use. Especially for trees, we found a strong influence of local land use on SCD and hence, population structures. The SCD of shrub species tends to be more related to species’ ecological preferences. Some of the shrub species may be characterized as ubiquitous species as their SCD is neither related to land use nor ecological preferences, indicating a high tolerance to disturbance. The observed results have implications on local woody species composition in relation to land use. According to this, we propose focusing on trees when developing appropriate local land use management strategies.