We evaluated the suitability of ELF-based assay (ELF: Enzyme-Labeled Fluorescence, Molecular Probes) as a tool for specific-detection of alkaline phosphatase (AP) activity in individual species of marine phytoplankton. Among 4 species of marine phytoplankton tested in the present culture experiments, the ELF-labeled cells of Karenia mikimotoi (Dinophyceae) and Skeletonema costatum (Bacillariophyceae) were simultaneously found with AP activity that was determined by using 4-methylumbelliferyl phosphate under the phosphorus-starved state but not found under the phosphorus-replete state. There were significant positive correlations between the percentage of ELF-labeled cells and AP activity of K. mikimotoi and of S. costatum. In contrast for Chattonella antiqua and Heterosigma akashiwo (Raphidophyceae) which do not produce AP, no ELF-labeled cells were found even under the phosphorus-starved state. Thus, ELF-based assay is considered to be useful for specific-detection of AP activity.