Fine-scale spatial genetic structure is increasingly recognized as an important factor in the studies of tropical forest trees as it influences genetic diversity of local populations. The biologic mechanisms that generate fine-scale spatial genetic structure are not fully understood. We studied fine-scale spatial genetic structure in ten coexisting dipterocarp tree species in a Bornean rain forest using microsatellite markers. Six of the ten species showed statistically significant fine-scale spatial genetic structure. Fine-scale spatial genetic structure was stronger at smaller spatial scales (≤ 100 m) than at larger spatial scales (> 100 m) for each species. Multiple regression analysis suggested that seed dispersal distance was important at the smaller spatial scale. At the larger scale (> 100 m) and over the entire sample range (0–1000 m), pollinators and spatial distribution of adult trees were more important determinants of fine-scale spatial genetic structure. Fine-scale spatial genetic structure was stronger in species pollinated by less mobile small beetles than in species pollinated by the more mobile giant honeybee (Apis dorsata). It was also stronger in species where adult tree distributions were more clumped. The hypothesized mechanisms underlying the negative correlation between clump size and fine-scale spatial genetic structure were a large overlap among seed shadows and genetic drift within clumped species.