Tropical forest fragmentation threatens biodiversity, yet basic information on population responses for major groups such as plants is lacking. Hypervariable genetic markers were used to reconstruct a population-level pedigree in fragmented tropical forest for the tree Symphonia globulifera. Though seedlings occurred only in remnant forest, the pedigree showed that most seedlings had been produced by sequentially fewer adults in pasture, creating a genetic bottleneck. The pedigree also implicated shifts in the foraging of animals that disperse pollen and seed in a secondary constriction of the bottleneck. These results suggest that tropical conservation strategies should anticipate complex, cryptic responses to fragmentation.