To assess the genetic consequences for a Neotropical tree of the loss of its main seed disperser, we compared the genetic structure of Inga ingoides in a site where the spider monkey (Ateles paniscus) was abundant and a site where it had been eliminated by subsistence hunting. Gene flow should be reduced in the site where the spider monkey is absent, and there should be a corresponding subpopulation differentiation of seedlings within the spatial range of the movements of these primates in the absence of between-site differences in allelic frequencies. At the microhabitat (family) scale, seedlings growing under parent plants should be genetically more related in the absence of the spider monkey than in its presence. Subpopulation differentiation was smaller where the spider monkey was present (four loci, FST = O.O11) than where it was absent (four loci, FST = O.053) for the first year of study, but not for the second year (three loci, FST = O.005 vs. O.003). The number of alleles in common among seedlings growing under parent plants was smaller in the presence of the spider monkey than in its absence, showing family genetic structure in the first generation for both years of study (Mann-Whitney, z = -2.17, p = 0.03 and z = -2.72, p = O.O06 for 1996 and 1997, respectively). This family genetic structure in the first generation should accelerate the development of population genetic structure. Development of genetic structure might result in demographic changes, one of which would be a fitness reduction if the species were self-incompatible, as suggested for Inga by available evidence. Large birds and mammals are the main targets of subsistence hunting in the Neotropics. Extinction of seed-dispersing frugivores may result in pronounced changes in the demographic and genetic structure of tree species in Neotropical forests.