In recent years, harmful algal blooms caused by dinoflagellates have become increasingly common in coastal waters throughout the world, causing negative impacts on human health, ecosystem quality and also affecting economic and commercial activities of the interested coastal areas. For the identification of potentially harmful microalgae, microscopy based methods are commonly used, but they are time consuming also requiring great taxonomic expertise. Thus, for the identification, counting and genetic characterization of these protists, more rapid, sensitive and specific molecular methods, such as real time PCR or microarray systems, have been developed and applied. Genus, species- specific primers and probes were designed on ribosomal DNA sequences (i.e. SSU, LSU and 5.8S genes, and ITS1 and ITS2 regions); they are suitable and highly informative molecular markers for studying the phylogeographic or phylogenetic relationships and the population genetic structure of the marine toxic dinoflagellates. The molecular methods have been applied to different kind of samples from cultured strains to field samples as surface seawater, macrophyte, sediment and aerosol samples in the Mediterranean Sea. These molecular systems proved to be effective tools for rapid, specific and sensitive detection and enumeration of potentially harmful microalgae, and thanks to their high throughput they can be applied in water monitoring programmes, to explore the community biodiversity and dynamics and to control and manage harmful blooms in marine coastal waters.