Raphidophytes have been associated with fish kill events in Japanese, European and U.S. coastal waters, and many produce toxins that can pose a threat to human health. The recognition of raphidophytes as HAB species in mid-Atlantic estuarine waters led us to initiate molecular phylogenetic analyses of these taxa and to develop real-time PCR assays for rapid detection of important species. The molecular studies and PCR detection methods will enhance ongoing taxonomic, toxicologic and ecological of these organisms and will be a useful tool in HAB monitoring programs.