Phosphoketolases (XFPs) are glycolytic enzymes present in several organisms belonging to the Eukarya and Bacteria domains. A total of 151 putative xfp genes were detected in 650 complete genomes available in public databases. Elimination of redundant sequences and pseudogenes rendered a final data set of 128 phosphoketolases, which was analyzed by phylogenetic methods. The distribution of xfp genes was uneven in most taxonomic groups, with the exception of the taxonomical division Lactobacillaceae, in which all the species studied harbored a putative xfp gene. Putative xfp genes were also present predominantly in Rhizobiales and Actinobacteria divisions, in which 23 out of 28 genomes and 23 out of 41 genomes contained at least one putative xfp homolog, respectively. Phylogenetic analyses showed clear discordance with the expected order of organismal descent even in groups where xfp is prevalent, such as Lactobacillaceae. The presence of putative paralogs in some organisms cannot account for these discrepancies; instead, these paralogs are most possibly xenologs. The results of the phylogenetic analyses, the distribution of xfp genes and the location of some xfp genes in plasmids are independent pieces of evidence that point to horizontal gene transfer as a major driving force in the evolution of phosphoketolases.