Alkaline phosphatases (APases) are important enzymes in organophosphate utilization. Three prokaryotic APase gene families, PhoA, PhoX, and PhoD, are known; however, their functional characterization in cyanobacteria largely remains to be clarified. In this study, we cloned the phoD gene from a halotolerant cyanobacterium, Aphanothece halophytica ( phoD _Ap ). The deduced protein, PhoD _Ap , contains Tat consensus motifs and a peptidase cleavage site at the N terminus. The PhoD _Ap enzyme was activated by Ca ²⁺ and exhibited APase and phosphodiesterase (APDase) activities. Subcellular localization experiments revealed the secretion and processing of PhoD _Ap in a transformed cyanobacterium. Expression of the phoD _Ap gene in A. halophytica cells was upregulated not only by phosphorus (P) starvation but also under salt stress conditions. Our results suggest that A. halophytica cells possess a PhoD that participates in the assimilation of P under salinity stress.