Pollen-mediated gene flow was analyzed in a small, fragmented, natural population of Fagus crenata Blume by surveying five microsatellite markers in seedlings derived from open-pollinated crosses. Paternity of 162 seedlings derived from two maternal trees was assigned by the maximum-likelihood method using CERVUS 2.0, and pollen dispersal patterns within the study site were determined. Most of the trees within the site sired seeds, although we found evidence of limited pollen-mediated gene flow from outside the stand; 92% of the matings that generated the seedlings occurred between trees within the population, and 8% of the matings were mediated by pollen derived from trees located outside the study site. Although the pollen-mediated gene flow within the site was not strongly limited, mating frequencies of paternal trees were found to be weakly negatively correlated with their distance from the mother trees, positively correlated with their stem diameter at breast height, and uncorrelated with their relatedness to the mother trees.