Cyanobacterial alkaline phosphatases (APases) play a key role in organophosphate utilization in freshwater. Tracking the distribution of APases could provide insights into the physiological response of phytoplankton to phosphorus nutrition. Extracellular APase PhoX, one of three prokaryotic APase families, is important for organophosphate utilization. Because the existing methods only give information on bulk APases activity, the speci c contribution of the PhoX is hardly evaluated. To develop an immunoassay for PhoX detection, the phoX gene of Microcystis aeruginosa PCC7806 was expressed in E. coli BL21 and the puri ed PhoX was used as a coated antigen for screening anti-PhoX nanobodies from an alpaca antibody library. After three rounds of panning, a nanobody 3H with the highest a nity was selected. Further tests showed 3H could speci cally bind to Microcystis PhoX and be used for PhoX detection by immunoblotting analysis. Then we constructed two different uorescent-labeled 3H, EGFP-3H (with an enhanced green uorescent protein, EGFP) and FITC-3H (with uorescein 5-isothiocyanate, FITC), as speci c uorescent dyes for PhoX. The uorescence staining tests with laboratory strains and water bloom samples showed that both uorescent-labeled nanobodies could visualize the distribution and evaluate relative expression levels of PhoX in Microcystis. The nanobody 3H could be a useful regent to develop uorescence immunoassays for in situ analyses of Microcystis PhoX.