The Atlantic forest is the biome most severely affected by deforestation in Brazil. Cabralea canjerana spp. canjerana is a dioecious tree species with widespread distribution in the Neotropical region. This species is considered a model to ascertain population ecology parameters for endangered plant species from the Atlantic forest. Fine-scale spatial genetic structure and pollen-mediated gene flow are crucial information in landscape genetics and evolutionary ecology. A total of 192 adults and 121 offspring were sampled in seven C. canjerana populations in the Southern Minas Gerais State, Brazil, to assess whether pollen-mediated gene flow is able to prevent spatial genetic structure within and among Atlantic forest fragments. Several molecular ecology parameters were estimated using microsatellite loci. High levels of genetic diversity (HE = 0.732) and moderate population structure (θ = 0.133) were recorded. No significant association between kinship and spatial distance amongst individuals within each population (Sp = 0.000109) was detected. Current pollen-mediated gene flow occurs mainly within forest fragments, probably due to short-distance flights of the pollinator of C. canjerana, and also the forest fragmentation may have restricted flight distance. The high levels of genetic differentiation found amongst the seven sites sampled demonstrated how habitat fragmentation affects the gene flow process in natural areas.