Animals are the principal vectors of dispersal for a large number of plant species. Unfortunately it is not easy to discern their movement patterns or the fate of their dispersed seeds. Many animals transport seeds by consuming them and then, some time later, defecating them. Others gather seeds and then store them for later consumption. Both circumstances lead to a set of seeds that have been dispersed in a clumped pattern, which offers a unique opportunity to assess seed movements. We introduce a novel approach that uses maternally inherited seed tissue to quantify the genetic structure of dispersed seed pools. This direct approach measures the genetic variability within and among seed pools, and estimates the scale of seed movement, without requiring a highly polymorphic battery of markers or the location and genotypes of all possible seed parents. We demonstrate this approach with the specific case of seed transport of valley oak (Quercus lobata) acorns by acorn woodpeckers (Melanerpes formicivorus). These territorial birds store acorns in drilled holes in the bark of trees, called granaries. We sampled stored acorns from different granaries, extracted DNA from the maternally inherited pericarp, and then assessed individuals for three microsatellite markers. We found extremely high genetic structure among granaries, a low number of effective seed donors per granary, and restricted seed movement. A maternity analysis performed on the same sample with seven microsatellites confirms acorn transport is limited to approximately 100-m radius. Our findings provide insight into the foraging and seed-dispersal behaviour of acorn woodpeckers, with an approach that can be widely extended to other systems.