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Aurelia spp. ephyrae have been reported to form blooms in sea cucumber aquaculture ponds in the Bohai and Yellow Seas. To identify the species, we carried out a genetic analysis of Aurelia spp. ephyrae and medusae based on mitochondrial 16S rRNA gene. Samples of four Aurelia sp. ephyrae populations were collected in sea cucumber aquaculture ponds and samples of four Aurelia sp. medusae populations were collected in coastal waters. Using a BLASTn search, we found that both the ephyrae collected in the aquaculture ponds and medusae collected in coastal waters belong to Aurelia coerulea . Seventeen haplotypes were recovered from the 16S rRNA gene. The overall haplotype diversity and nucleotide diversity of the 166 A . coerulea individuals were 0.686％ and 0.329％, respectively, indicating high haplotype diversity and low nucleotide diversity. Moreover, the haplotype diversity of ephyrae populations were generally lower than that of medusae populations with close sampling points. The genetic differentiation between ephyrae populations collected in the sea cucumber aquaculture ponds and A . coerulea medusae collected in coastal waters was not significant, suggesting the ephyrae populations in the sea cucumber culture ponds were part of the same genetic group as the medusae populations in the coastal waters. Phylogeographic analysis of the 16S rRNA region revealed that there was no significant correlation between the haplotypes and the geographic distribution of populations. Pairwise fixation index values showed significant genetic differentiation and limited gene flow between A . coerulea population of Weifang and other locations.