Abstract
Accurate species identification is required to trace, monitor and limit the distribution of harmful shell boring species of the genus Polydora, which have been transported worldwide accompanying commercially important mollusk species. Morphological identification of species in the polydorid complex is difficult because of close similarities, therefore, nuclear 18S rRNA gene sequences were used for the first time to distinguish among the three serious aquaculture pests Polydora brevipalpa, Polydora uncinata, and Polydora aura, from Japan and Australia. The analysis revealed new intraspecific pigmentation variation and confirmed that P. uncinata and P. aura are closely related, possessing special notochaetae on the posterior chaetigers, while P. brevipalpa is a sister taxon to these two species. Polydora brevipalpa and P. uncinata share characteristic black-bar pigmentation on their palps, but they apparently are not part of the same clade.
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