The complete collection of evolutionary histories of all genes in a genome, the so-called phylome, constitutes a valuable source of information. Traditionally prevented by large demands on time and computer power, the reconstruction of phylomes is now feasible thanks to recent developments in computers and algorithms. In order to provide a publicly available repository of complete phylomes that allows researchers to access and store large-scale phylogenomic analyses, we have developed PhylomeDB. PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. All phylomes in the database are built using a high-quality phylogenetic pipeline that includes evolutionary model testing and alignment trimming phases. For each genome, PhylomeDB provides the alignments, phylogentic trees and tree-based orthology predictions for every single encoded protein.