Seventeen natural populations in Costa Rica and Panama were used to asses gene flow and geographic patterns of genetic variation in this tree species. Gene flow analysis was based on the methods of rare alleles and FST (Index of genetic similarity M), using the only four polymorphic gene loci among 22 investigated (PGI-B, PGM-A, MNR-A and IDH-A). The geographic variation analysis was based on Pearson`s correlations between four geographic and 14 genetic variables. Some evidence of isolation by distance and a weak gene flow among geographic regions was found. Patterns of clinal variation in relation to altitude (r = -0.62 for genetic diversity) and latitude (r= -0.77 for PGI-B3) were also observed, supporting the hypothesis of isolation by distance. No private alleles were found at the single population level.