To detect Cochlodinum polykrikoides in long-term monitoring and high-throughput sampling projects using an integrated sandwich hybridization and nuclease protection assay (NPA-SH). The specificity of the probes was verified with individual and mixed cultures as well as field collection, and the quantity of C. polykrikoides determined by NPA-SH analysis showed a good correlation with that determined by cell-counting with a light microscope. In addition a standard curve for C. polykrikoides was established to represent the correlation between optical absorbance in the NPA-SH assay and cell density. This approach provides an efficient alternative to traditional, morphology-based methods for the rapid identification and quantification of harmful algal species and could be used to monitor phytoplankton in field surveys.