Incorporating molecular tools into routine HAB monitoring programs: Using qPCR to track invasive Prymnesium

► We modified a qPCR method for quantifying densities of Prymnesium parvum in nature. ► qPCR density estimates were similar to microscopy-based estimates. ► qPCR detected P. parvum where it previously had gone undetected by microscopy. ► qPCR reduces time and error, and increases detection limit for P. parvum monitoring.