The global increase in frequency and intensity of harmful algal blooms (HABs) has led to more frequent incidence of seafood-borne illnesses and adverse impacts on natural resources. In response, public health agencies worldwide have mobilized to initiate HAB monitoring programs. To meet this demand, innovative analytical techniques are being developed that provide rapid and reliable detection of the causative organisms and the toxins produced. Modifications to conventional chromatography and mass spectrometry have greatly improved sensitivity and selectivity of these methods toward naturally occurring phycotoxins. Bioassay techniques using live organisms are giving way to molecular and cellular methods that measure the toxicologically significant activity of the toxin molecules. Molecular probes are being applied to distinguish species-specific RNA and DNA sequences for rapid identification of HAB-causing organisms. The direction of this new technology is to develop rapid and reliable screening methods for phycotoxins and the causative organisms to provide protection for public health, aquaculture, and natural resources. New methods also are being developed for detecting minute amounts of toxin molecules in microenvironments, leading to understanding the toxicokinetics and toxicological functions of the toxins.