Phytate, the most abundant organic phosphorus compound in soil, dominates the biotic phosphorus input from terrestrial runoffs into aquatic systems. Microbial mineralization of phytate by phytases is a key process for recycling phosphorus in the biosphere. Bioinformatic studies were carried out on microbial genomes and environmental metagenomes in the NCBI and the CAMERA databases to determine the distribution of the four known classes of phytase in the microbial world. The beta-propeller phytase is the only phytase family that can be found in aquatic environments and it is also distributed in soil and plant bacteria. The beta-propeller phytase-like genes can be classified into several subgroups based on their domain structure and the positions of their conserved cysteine residues. Analysis of the genetic contexts of these subgroups showed that beta-propeller phytase genes exist either as an independent gene or are closely associated with a TonB-dependent receptor-like gene in operons, suggesting that these two genes are functionally linked and thus may play an important role in the cycles of phosphorus and iron. Our work suggests that beta-propeller phytases play a major role in phytate-phosphorus cycling in both soil and aquatic microbial communities.