The internal transcribed spacer (ITS) region of the nuclear rDNA was used to discriminate among cultured marine raphidophytic algal species of Chattonella antiqua, C. subsalsa, Fibrocapsa japonica, Heterosigma akashiwo and Olisthodiscus luteus. These wall-less algae can be very difficult to identify from natural water samples due to their fragile nature and pleomorphic morphology. Several of these algae have been associated with massive finfish kills throughout the world, therefore positive identification is of great importance. Species-specific diagnostic PCR fragment sizes resulted from three- primer amplification reactions and can reproducibly detect as few as five cells per sample. Recently, an active area of ecological research has been retrospective studies from archival material to determine population dynamics and species diversity. The use of these PCR primers with fresh cultures as well as archived material containing either formalin or Lugol s iodine has been successful. This is a valuable technique for detection and discrimination among marine Raphidophyceae particularly when cells can not be identified morphologically.