Fragmentation threatens biodiversity globally. Manilkara maxima (Sapotaceae) is listed by the IUCN as threatened and is an economically and ecologically important tree species endemic to the Atlantic forest of southern Bahia, Brazil, a biodiversity hotspot. The objectives of this study were to examine the effect of fragment size on density and genetic diversity of this threatened species. We surveyed and sampled 222 individuals across 2 large forest sites and 1 site comprising 8 small fragments. We focused on 5 microsatellite loci that provided comparable genetic information (average 21 alleles locus−1) as 2 congeners in other studies. Fragment size accounted for 71 and 56% of density variation in adult and sapling trees, respectively, but did not account for genetic variation. Rather, density accounted for 80% of allelic diversity and 70% of allelic richness in both life stages. The lack of relationship between genetic diversity and fragment size was driven in part by a co-variation in density and genetic diversity in 25 ha fragments. These small forests can have high densities of M. maxima, and in turn, can have as much genetic diver- sity and conservation value as larger fragments. However, the larger fragments are of unique con- servation value because they hold the greatest number of reproductively mature individuals, the ones necessary for the recruitment of new individuals. Our results suggest that relatively high lev- els of gene flow are contributing to the high genetic diversity of saplings found in some of the small fragments.