Which nutrient or factor limits primary production in different marine waters continues to be the subject of research and debate among oceanographers. Current techniques for studying phytoplankton physiology such as measurements of biochemical activities, nutrient addition bioassays and determination of photosynthetic efficiency are generally capable of assessing the physiology of the bulk community but suffer from a lack of specificity. Thus, interest is increasing in the development of single-cell methods for monitoring in situ physiology. Cell-specific techniques are particularly helpful for studying and monitoring populations of harmful species in mixed assemblages.An antibody-based assay for identifying phosphate stress in the dinoflagellate Prorocentrum minimum was developed. Antiserum was generated against a cell-surface alkaline phosphatase purified from P. minimum.Western screening indicated that the antiserum reacted with phosphate-stressed cells but not nitrate-stressed or phosphate-replete cells in culture. Immunodepletion using either pre-immune or primary antisera cross-linked to agarose beads confirmed the target protein was an alkaline phosphatase. At this juncture the antiserum appears specific for phosphate-regulated proteins in P. minimum as there is no discernible cross reaction with closely related P. micans in western blots. In addition to westerns an immunofluorescence protocol was developed to screen field populations. This technique complements our recent development of ELF-97-labeling as a tool for examining P. minimum phosphate stress in field populations.This is the first antibody-based method developed for monitoring cell-specific physiology in a dinoflagellate. The method described here may serve as a model for developing similar tools in other species of dinoflagellates.