Under the isolation-by-distance model, the strength of spatial genetic structure (SGS) depends on seed and pollen dispersal and genetic drift, which in turn depends on local demographic structure. SGS can also be influenced by historical events such as admixture of differentiated gene pools. We analysed the fine-scale SGS in six populations of a pioneer tree species endemic to Central Africa, Aucoumea klaineana. To infer the impacts of limited gene dispersal, population history and habitat fragmentation on isolation by distance, we followed a stepwise approach consisting of a Bayesian clustering method to detect differentiated gene pools followed by the analysis of kinship-distance curves. Interestingly, despite considerable variation in density, the five populations situated under continuous forest cover displayed very similar extent of SGS. This is likely due to an increase in dispersal distance with decreased tree density. Admixture between two gene pools was detected in one of these five populations creating a distinctive pattern of SGS. In the last population sampled in open habitat, the genetic diversity was in the same range as in the other populations despite a recent habitat fragmentation. This result may due to the increase of gene dispersal compensating the effect of the disturbance as suggested by the reduced extent of SGS estimated in this population. Thus, in A. klaineana, the balance between drift and dispersal may facilitate the maintenance of genetic diversity. Finally, from the strength of the SGS and population density, an indirect estimate of gene dispersal distances was obtained for one site: the quadratic mean parent-offspring distance, sg, ranged between 210 m and 570 m.