Phosphorus is an essential macro-nutrient supporting biological productivity in natural and agricultural ecosystems alike. Phosphorus chemical pathways in soil are complex, but organo-phosphorus compounds typically constitute a major component. This organic pool is turned over by a suite of microbial phosphohydrolase enzymes (alkaline and non-specific acid phosphatases and phytases) which cleave phosphoester (P-O) bonds, releasing assimilable orthophosphate for both the soil microbiome and plant communities. Understanding how edaphic factors and soil management can influence phosphohydrolase distribution is important to understanding both environmental biogeochemical processes and managing agricultural fertility using more benign approaches. Shotgun metagenomic methods indicate that alkaline phosphatase phoD and phoX, class A and C non-specific acid phosphatases and β-propeller phytase genes are the most abundant and responsive genes in soil, but that the relative abundance of each group within communities fluctuates. These shifts do not appear to be dependent upon localized phosphorus bioavailability: in a long-term fertilization experiment under wheat in the UK, genes respond to edaphic factors, particularly exchangeable calcium which acts as a co-factor for several alkaline phosphatase and phytase enzymes. In a second long-term phosphorus fertilization study under Maize and Sorghum in Brazil, gene abundance responds to plant species, being more abundant under Sorghum than Maize. These same genes are present in metagenomes generated from geographically- and ecologically-distinct soils and marine sediments from around the globe. The phylogenetic diversity of these genes is highly conserved and the sequences present are consistent with horizontal genetic transfer event predictions based upon bipartition dissimilarities between PHO gene and 16S rRNA phylogenies. Currently available data suggests the following hypothesis: phosphohydrolase genes are maintained within microbiomes by horizontal genetic transfer processes, but are selected for within particular environments based upon, as yet, unidentified plant associations or edaphic factors.