Selective logging is known to alter the structural and community composition of tropical forests and may disrupt plant-frugivore interactions. We hypothesized that even after a sufficient period of recovery, logged areas will not possess as complete a suite of species as an unlogged forest, the differences being more marked for biotically-dispersed species. Species of this functional group are expected to occur at lower densities, have lower species richness and diversity, and be smaller in logged forests. To quantify structural and functional differences in tree communities, we sampled 120 randomly placed plots, 60 each in logged and unlogged forest sites. We found significant differences in species richness and diversity between logged and intact forest. Within biotically-dispersed species, bird dispersed species showed a significant reduction in species richness. Consistent with previous studies, trees in logged forests were smaller, although overall density was not different between the two treatments. We posit that selective logging might have pervasive effects on functional aspects of tropical tree communities, which appear to persist even after two decades of logging cessation.