Until now all amphioxus living in Xiamen waters have been regarded as Branchiostoma belcheri without any suspicion. However, a study based on Cyt b gene sequence comparisons of Branchiostoma belcheri (Oucuo in Xiamen waters) and Branchiostoma belcheri tsingtauense (Japanese waters) showed unexpected high divergence suggesting that the taxonomic status of Xiamen amphioxus should be reevaluated. In order to clarify this issue, we collected the animals from two sampling sites (Oucuo and Huangcuo in Xiamen waters), and compared their morphologies (meristic and non-meristic) as well as the complete sequences of their 12S rRNA genes. The samples could be distinguished by six of the non-meristic traits and five of the meristic traits. Moreover, the genetic distance based on 12S rRNA gene between Oucuo and Huangcuo amphioxus is 21.13%, but that between Huangcuo and Japanese amphioxus is only 0.56%. Our results suggest that original subspecies B. belcheri tsingtauense should be elevated to species level, becoming B. tsingtauense. Therefore, two species of genus Branchiostoma are living in Xiamen waters. One is the original species B. belcheri (Oucuo) and the other is B. tsingtauense (Huangcuo).
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