Anthropogenic pressures such as hunting are increasingly driving the localized functional extinctions of all or most large and medium-sized wildlife species in tropical forests, a phenomenon broadly termed defaunation. Concurrently in these areas, smaller-bodied wildlife species benefit from factors such as competitive release and experience population increases. This transformation of the wildlife community can impact species interactions and ecosystem services such as seed dispersal and seed-mediated geneflow with far reaching consequences. Evidence for negative genetic effects following defaunation is well-documented in large-seeded plants that require large frugivores for long distance seed dispersal. However, how defaunation affects small-seeded (< 1.5cm diameter) plants, which are dispersed by frugivores with a wide range of body-sizes and responses to anthropogenic threats, is not well understood. To better understand the reach of defaunation’s impacts on tropical plant communities, we investigated spatial and genetic patterns in a hyperabundant small-seeded palm, Euterpe precatoria in three sites representing distinct defaunation levels. We found significantly higher fine-scale spatial genetic structure among nearest-neighbor seedlings in the defaunated site and in the recovering, partially defaunated site relative to the faunally-intact site. Defaunation was associated with shorter distances between seedlings and adults and lower genetic distance between adult and seedling cohorts. No effects were detected on inbreeding and genetic diversity; however, we caution that trends we detected indicate that defaunation influences the spatial distribution of genetic variation even in small-seeded plants that inherently have a broad suite of seed dispersal agents, and this could lead to negative downstream effects on genetic diversity.