Soluble reactive phosphorus is the main form of phosphorus directly available for phytoplankton in natural waters, and the organophosphate mineralization catalyzed by bacterial alkaline phosphatases maintains the supply of soluble reactive phosphorus. We summarized the species and subcellular location of bacterial alkaline phosphatases and found that PhoA, PhoX and PhoD were the main phosphatase species. Over 50% of PhoX were distributed outside of bacterial cells, which is particularly important for the regeneration of soluble reactive phosphorus in natural waters. The research progress in communities of alkaline phosphatase encoding bacteria and the environmental factors influencing the expression of alkaline phosphatase encoding genes were also reviewed. We compared and analyzed the characteristics and developing trend of identification methods towards bacterial communities generating alkaline phosphatases. Most of studies about bacterial alkaline phosphatase-encoding genes were focused on oligotrophic marine ecosystems, and little was on the lake ecosystems which are also facing the phosphorus-limiting problem. Further researches should construct the bacterial metagenomic databases for certain eutrophic lakes to provide basis for build the methodology for bacterial alkaline phosphatases and affiliated encoding genes in freshwater ecosystems, which are beneficial to understand the microbial mechanisms driving frequent cyanobacterial blooms in lakes.