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ABSTRACT Anthropogenic pressures such as hunting are increasingly driving the localised functional extinctions of large‐ and medium‐sized wildlife in tropical forests, a phenomenon broadly termed ‘defaunation’. Concurrently in these areas, smaller‐bodied species benefit from factors such as competitive release and increase in numbers. 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 plants with small or medium‐small seeds (< 1.5 cm), which tend to be consumed and dispersed by frugivorous mutualists of a range of body sizes and responses to anthropogenic threats, is not well understood. To better understand defaunation's impacts on tropical plant communities, we investigated spatial and genetic patterns in a hyperabundant medium‐to‐small‐seeded palm,Euterpe precatoriain three sites with different defaunation levels. Results indicate that defaunation is associated with higher fine‐scale spatial genetic structure among seedlings and increased spatial clustering within seedling cohorts and between seedlings and conspecific adults, as well as a reduction in nearest‐neighbour distances between seedlings and conspecific adults. There were no clear effects on inbreeding or genetic diversity. However, we caution these trends may indicate that defaunation reduces seed dispersal services for species previously presumed to be robust to deleterious effects of losing large frugivores by virtue of having smaller seeds and broad suites of dispersal agents, and negative downstream effects on genetic diversity could occur.