The cosmopolitan diatom Chaetoceros is well-known as one of the most abundant and species-rich microalgal genera, and considered important from the viewpoints of biogeochemistry, marine ecology, biodiversity and so on. Thus, accurately distinguishing Chaetoceros species is essential in understanding the microbial ecology of aquatic environments. However, precise identification of Chaetoceros at the species level is extremely difficult, which makes the comprehension of the ecological dynamics of this diatom genus practically impossible. In this study, in order to overcome this problem, we applied polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) to distinguish 18 isolates of Chaetoceros species targeting the rbcL region of chloroplast DNA encoding RubisCO large subunit. Suitable restriction enzymes to distinguish the PCR samples were selected based on rbcL DNA sequences. As a result, the tested Chaetoceros isolates were successfully distinguished by treatment with restriction enzymes, DdeI, Csp45I and RsaI. This result indicates that PCR-RFLP method is applicable for identification of hard-to-identify diatoms groups.

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