Dense raphidophyte blooms are a cause of mass fish mortalities in coastal areas throughout the world. The recent dramatic global increase in aquaculture, especially fish farming, has led to a heightened requirement for knowledge on characterization and toxigenicity of raphidophyte blooms. In the Mediterranean, raphidophytes form annual blooms in coastal waters, thereby posing a threat to fish aquaculture. We investigated a mixed bloom event involving the raphidophytes Chattonella sp. and Fibrocapsa sp. on the Adriatic coast of Italy, including molecular genetic, morphological and ecological aspects. Light and electron microscopy revealed one of species as Chattonella subsalsa as described by Biecheler (1936). Nevertheless, genetic markers for nuclear and ribosomal DNA (LSU, SSU, ITS, psaA and RubisCo) differentiated this Chattonella, and with less distinctness, Fibrocapsa sp., from other known strains of the respective genera. Phenotypic differences among isolated clones were determined from profiles of polyunsaturated fatty acids (PUFAs) and activity of reactive oxygen species (ROS), which are putatively responsible for ichthyotoxicity. Strains were bioassayed with a fish erythrocyte lytic assay and the brine shrimp Artemia salina test. The relationship (if any) between toxicity and phenotypic and genotypic characteristics is complex and not yet resolved.