PCPS is an R package for exploring phylogenetic eigenvectors across metacommunities. It offers a set of functions for analyzing principal coordinates of phylogenetic structure (PCPS), allowing analysis of phylogenetic signal in ecological traits of species at the metacommunity level, and the association between each PCPS and environmental, spatial and historical factors. The package is a flexible solution for exploring the distribution of major phylogenetic lineages across ecological or biogeographic gradients. The package is freely available on the CRAN official web server for R.