The Subtropical Atlantic Forest is located in a large part of the State of Minas Gerais, and the riparian forest is one of its main physiognomies. Due to its performance as ecological corridor and genetic reservoir, this kind of forest assures the conservation and perpetuation of many species. As the riparian environments possess peculiar characteristics, there is the occurrence of typical species in these areas. Among them, Calophyllum brasiliense outstands due to its ecological plasticity and preference for settling waterlogged soils, being considered specialist in habitat. Thus, in order to assess and understand patterns of genetic variability inter and intra population of C.brasiliense, as well as its spatial distribution and reproductive system, three habitats were chosen: Riparian Forest, Swampy Forest and Gallery Forest. From each habitat, two populations were taken, being sampled 60 trees in each. For the reproductive system study, fruits were collected from two habitats (Riparian Forest and Gallery Forest). Results obtained by enzyme electrophoresis analysis showed a high heterozygosity for this species, Ĥо ranging from 0.355 to 0.468 and from 0.441 to 0.493 for the reproductive trees and progenies, respectively. The genetic structure analysis indicated the occurrence of intra and inter population ˆ endogamy for Riparian Forest ( ˆ = 0.114; F = 0.191) and for Swampy Forest f ˆ ( ˆ = 0.060; F = 0.185). Most of the genetic variability was distributed within f ˆ each population and the gene flow ( Nm ) was low. The effective size estimative ˆ showed that only in the populations sampled in the Gallery Forest N value e (130 individuals) was higher than that of the sampled individuals (n = 120). The coancestry coefficient estimative showed that the closest trees presented higher genetic similarity. The space distribution of C.brasiliense in the three habitats, showed to be highly correlated with the high moisture of the soils, directly influencing its genetic variability and gene flow. The cluster analysis did not detect a possible relation between the occurrence habitats and the genetic identity, nor found a correlation between the geographical distance and genetic identity (rm = 0.063). The progenies analysis showed that the species is ˆ allogamous ( t m = 0.996) in the populations of the Riparian Forest and 0.974 in the population of the Gallery Forest. The reproductive system indicated that for the populations sampled in the Riparian Forest, most of the progenies were ˆ originated by biparental crossings ( PIC = 54,8%). As for the population sampled in the Gallery Forest, most of its progenies were originated by random crossings ˆ ( PMI = 70.3%). Thus, independent of the habitat, it is necessary the conservation of natural populations of C. brasiliense, since this species demonstrates certain fragility to the factors that threaten its genetic variability, such as the degradation of its populations and lack of connection among them.