Alkaline phosphatases (APases) play a crucial role in phosphorus (P) metabolism and regulation, but their physiological functions largely remain unclear in cyanobacteria. Here, we identified four putative APase genes, designated as phoA-709, phoD1-709, phoD2-709, and phoS-709, in the cyanobacterium Anabaena sp. FACHB 709, and investigated their response to inorganic phosphate (P-i) starvation. With the exception of phoD2-709, three other APase genes were expressed at a constant and relative low level in P-i-replete medium, whereas the expression of all four APase genes was elevated in response to P-i starvation but phoA-709 significantly. However, disruption of phoA-709 did not affect the total APase activity but caused the expressional up-regulation of phoD1-709 and phoS-709 under P-i-sufficient and P-i-limiting conditions. These suggest that, the four APases of Anabaena sp. FACHB 709 are involved in P metabolism and regulation, and PhoA-709 is the main, yet dispensable, APase.