Morphological and SRAP markers were used to analyze the phylogenetic relationship and genetic diversity of eight populations of Moerella iridescens in Zhejiang Province, especially focusing on Yueqing bay. The populations in Yueqing, Wenling and Taizhou had the similar morphologies, but they had more difference with the populations in Ningbo and Zhoushan. The genetic diversity of population in Yueqing was higher than that in Zhoushan or Ningbo. All populations collected from Yueqing were clustered together, showing that they had smaller genetic distance and higher genetic similarity. The similarity in both morphological and SRAP data reflects the geographical relationship among the eight populations. It should be noted that aquaculture population of M. iridescens collected from Yueqing was more similar with that from Ningbo, not with those from Yueqing, reminding us to avoid possible germplasm hybrid of M. iridescens in Yueqing bay.