Abstract: Polydora lingshuiensis and P.websteri were compared for precise identification by techniques of morphology and molecular biology. Their geographical distributions were also investigated. Morphologically, P.lingshuiensis are differentiated from P.websteri in that P.lingshuiensis have one median antenna on the caruncle and one concavity at subterminal end of major spine, whereas P.websteri have no median antenna, and have lateral flange on major spine. Distance analyses reveal that the interspecific distance between P.lingshuiensis and P.websteri is obviously longer than their intraspecific distance based on nucleus 18S gene, mitochondrial COⅠ and Cyt b gene. Distance ratio between interspecific and intraspecific polydorins is much greater based on mitochondrial COⅠ and Cyt b gene than nucleus 18S gene. Mitochondrial COⅠ and Cyt b gene have wider barcoding gap and higher resolution than nucleus 18S gene, so they are more suitable for assistant identification of morphologically similar polydorins. P.lingshuiensis and P.websteri are of low host-specificity and widespread along China′s coastal waters. Their transmissions may be closely related to the breeding manner and commercial transportation of their hosts.