Mating system and pollen flow are two key elements to understand the genetic structure of tree species. Mating and pollen-dispersal patterns of a low-density population of bat pollinated Hymanea courbaril were examined before logging in a 546-ha plot in the Brazilian Amazon. The multilocus genotypes of nine microsatellite loci were determined for 130 adult-trees and 367 seeds collected from 20 seed-trees. Mating system analysis, using mixed-mating model and paternity analysis showed that the studied population is perfectly outcrossed (t(m)= 1.002), and probably self-incompatible. However, significant deviations from random mating were detected for mating among relatives (t(m) - t(s) = 0.096, P < 0.05) and correlated matings (r(p) = 0.289, P < 0.05), indicating inbreeding in the population and that part of offspring are full-sibs (28.9%). Inbreeding was reflected in the positive and significant fixation index observed in adult trees (F = 0.137, P < 0.05), although no significant inbreeding was detected in offspring (F = 0.074, P > 0.05). The effective number of pollen donors mating with each seed-tree was determined to be low (N-ep approximate to 4). The average of pollen flow distance was measured inside of the plot by both paternity (827 +/- 429 m) and TwoGener analysis (115-363 m). However, this underestimated pollen dispersal distance, since the detected rate of pollen immigration inside of the plot was high (55%). The observed long-pollen dispersal distance is probably related to pollination by bats and the low density of reproductive trees in the site.