Hunting affects a considerably greater area of the tropical forest biome than deforestation and logging combined. Often even large remote protected areas are depleted of a substantial proportion of their vertebrate fauna. However, understanding of the long-term ecological consequences of defaunation in tropical forests remains poor. Using tree census data from a large-scale plot monitored over a 15-year period since the approximate onset of intense hunting, we provide a comprehensive assessment of the immediate consequences of defaunation for a tropical tree community. Our data strongly suggest that over-hunting has engendered pervasive changes in tree population spatial structure and dynamics, leading to a consistent decline in local tree diversity over time. However, we do not find any support for suggestions that over-hunting reduces above-ground biomass or biomass accumulation rate in this forest. To maintain critical ecosystem processes in tropical forests increased efforts are required to protect and restore wildlife populations.