In savanna vegetation, trees and their canopies provide an important, but scattered habitat. Seeds of plants growing under these nurse trees often are dispersed by animals, especially birds. In the present study, we investigated the influence of tree size and frugivore dispersal on the genetic variation of the subcanopy species Pollichia campestris, using amplified fragment length polymorphisms (AFLP). Considering the individuals under each nurse tree as subpopulations, we found the genetic variation within subpopulations to be positively correlated with the size of the respective canopy tree. Genetic variation was very low among, but high within subpopulations (ΦPT = 0.026, P = 0.18). We conclude that the low genetic variation among subpopulations is due to effective and directed dispersal (dispersal from one canopy to another) by legitimate and frugivorous dispersal agents.