We investigated the phylogeny of 93 sequenced strains within the Pseudomonas fluorescens complex using state-of-the-art whole-genome sequence-based methods such as the Genome Blast Distance Phylogeny approach. As a result we divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH; http://ggdc.dsmz.de) identified 69 species and 75 subspecies among the 93 strains. The eight groups corresponded to clustering with a threshold of 31.8% dDDH. The article was published in PLoS ONE.