Bacterial alkaline phosphatases (APases) are important enzymes in organophosphate utilization in the ocean. The subcellular localization of APases has significant ecological implications for marine biota but is largely unknown. The extensive metagenomic sequence databases from the Global Ocean Sampling Expedition provide an opportunity to address this question. A bioinformatics pipeline was developed to identify marine bacterial APases from the metagenomic databases, and a consensus classification algorithm was designed to predict their subcellular localizations. We identified 3,733 bacterial APase sequences (including PhoA, PhoD, and PhoX) and found that cytoplasmic (41%) and extracellular (30%) APases exceed their periplasmic (17%), outer membrane (12%), and inner membrane (0.9%) counterparts. The unexpectedly high abundance of cytoplasmic APases suggests that the transport and intracellular hydrolysis of small organophosphate molecules is an important mechanism for bacterial acquisition of phosphorus (P) in the surface ocean. On average, each marine bacterium possessed at least one suite of uptake of glycerol phosphate (ugp) genes (e.g., ugpA, ugpB, ugpC, ugpE) for dissolved organic phosphorus (DOP) transport, but only half of them had ugpQ, which hydrolyzes transported DOP, indicating that cytoplasmic APases play a role in hydrolyzing transported DOP. The most abundant heterotrophic marine bacteria, α- and γ-Proteobacteria, might hydrolyze DOP outside the cytoplasmic membrane, but the former could also transport and hydrolyze DOP in the cytoplasm. The abundant extracellular APases could provide bioavailable P for organisms that cannot directly access organophosphates, and thereby increase marine biological productivity and diversity.