Hunting with firearms decimates primates of large and medium body size (>2 kg) that disperse the seeds of large-seeded trees. In continuous, un-fragmented forests of southeastern Peru regularly hunted with firearms for 30-40 years, large primates are extirpated and medium-sized (medium) primates are reduced 61% compared with protected forests. At hunted sites seedlings and small juveniles (<1 m height) of trees dispersed by primates heavier than 2 kg are reduced 46%, a loss of one species m-2, and abiotically-dispersed plants are 284% more common, adding eight individuals m-2, compared with protected forests. Here we provide evidence consistent with the long-held prediction that commercial hunting changes plant communities. We show that the composition of seedling and small juvenile tree communities that ultimately regenerate future forests differs markedly in forests hunted with firearms compared with protected forests. This opens the possibility of shifts in tree species composition, even in hunted forests that are not logged or fragmented, towards forests dominated by trees dispersed by wind or non-game animals. © 2008 Elsevier Ltd. All rights reserved.