Hunting in tropical forests decimates large mammals, and this may have direct and indirect effects on other trophic levels and lead to trophic cascades. We compared replicated sites of hunted and protected forests in southeastern Nigeria, with respect to community composition of primates, other mammals, birds, plant seedlings, and mature trees. We make predictions regarding the community composition at the different trophic levels. In forests where large primates are rare, we hypothesize that their ecological role will not be fully compensated for by small frugivores. We apply multivariate methods to assess changes in community composition of mammals, birds, and seedlings, controlling for any differences between sites in the other groups, including mature trees. Medium and large (4–180 kg) primates were much rarer in hunted sites, while porcupine and rock hyrax increased in abundance with hunting. In contrast, the community composition of birds was similar in both types of forests. Seedling communities were significantly related to the community composition of mammals, and thus strongly affected by hunting. In protected forests primate dispersed plant seedling species dominated, whereas in hunted forests the seedling community was shifted towards one dominated by abiotically dispersed species. This was probably both a consequence of reduced seed dispersal by primates, and increased seed predation by rodents and hyrax. Hence we found no evidence for buffering effects on tree regeneration through functional compensation by non-hunted animals (such as birds). Our results highlight how seedling communities are changed by the complex plant–animal intera ctions, triggered by the loss of seed dispersers. The results predict a rarity of primate-dispersed trees in future tropical forest canopies; a forest less diverse in timber and non-timber resources.