The genus Prochlorococcus is globally abundant and dominates the total phytoplankton biomass and production in the oligotrophic ocean. The single species, Prochlorococcus marinus, comprises six named ecotypes. Our aim was to analyze the taxonomic structure of the genus Prochlorococcus. We analyzed the complete genomes of 13 cultured P. marinus type and reference strains by means of several genomic taxonomy tools (i.e., multilocus sequence analysis, amino acid identity, Karlin genomic signature, and genome to genome distance). In addition, we estimated the diversity of Prochlorococcus species in over 100 marine metagenomes from all the major oceanic provinces. According to our careful taxonomic analysis, the 13 strains corresponded, in fact, to ten different Prochlorococcus species. This analysis establishes a new taxonomic framework for the genus Prochlorococcus. Further, the analysis of the metagenomic data suggests that, in total, there may only be 35 Prochlorococcus species in the world's oceans. We propose that the dearth of species observed in this study is driven by high selective pressures that limit diversification in the global ocean.