Fundamental hypotheses concerning the maintenance and generation of diversity in ecological communities posit a central role for the differences among plants in metabolites that function as defenses against herbivores and pathogens. Yet the vast diversity of plant chemical defenses has traditionally precluded community-level studies of chemical ecology. Here, I use untargeted metabolomics based on mass spectrometry to identify, classify, and compare the structures of >10,000 unique foliar metabolites from 314 tree species recorded in the BCI 50-ha forest dynamics plot and >20,000 metabolites from 906 species sampled in 16 1-ha forest plots representing an elevational gradient in the tropical Andes in Bolivia. I ask whether species metabolomes define niches by i) contributing to density-dependent mortality driven by enemy-mediated competition and ii) varying over elevational and environmental gradients. I find that seedling survival is reduced by heterospecific neighbors that are similar with respect to secondary metabolites, but enhanced by similarity to primary metabolites on BCI. Further, chemical dissimilarity of co-occurring species declines with elevation but increases with species diversity in the tropical Andes, whereas chemical properties associated with light absorbance, polarity, and topological complexity vary in ways that suggest variation in the sources of selection on plant metabolomes over elevational gradients.