Fragmentation of tropical forests influences abiotic and biotic processes that affect the genetic structure of plant populations. In forest fragments, edge effects, i.e. changes of abiotic and biotic factors at forest edges, may be prevalent. In two forest fragments (c. 200 ha at c. 2450 m asl) of tropical montane forest in Bolivia, sympatric populations of the dioecious tree species Clusia sphaerocarpa and C. lechleri were used as case study species to compare genetic diversity and small-scale genetic structure (SGS) between edge and interior habitats. Eight microsatellite markers were employed to genotype 343 individuals including adults, juveniles and seedlings of C. sphaerocarpa and 196 of C. lechleri. Genetic differentiation was found between habitats in both species (ΦRT = 0.071 for C. sphaerocarpa and ΦRT = 0.028 for C. lechleri) and among ages in C. sphaerocarpa (ΦRT = 0.016). Overall, SGS was weak but significant with more pronounced SGS in C. lechleri (Sp = 0.0128) than in C. sphaerocarpa (Sp = 0.0073). However, positive spatial genetic autocorrelation extended only up to 10 m. For C. sphaerocarpa, SGS was stronger in seedling and juvenile stages than in adults and in the forest interior than at forest edges. Our results show that edge effects can extend to the genetic level by breaking-up local genetic structures, probably due to increased gene flow and enhanced pollination and seed-dispersal interactions at forest edges.