Being a major component of coastal zooplankton assemblages, hydromedusae play a key role in material recycling and energy flow of marine ecosystems in Taiwan Strait.However, Species identification is challenging for this group due to their phenetic simplicity.DNA barcoding provides an efficient method for species identification.In the present study, 102 COI and 118 16S sequences from 32 hydromedusae species were amplified.A neighbor-joining phylogenetic tree was constructed based on Kimura 2-parameter genetic distance and further studied using Klee-diagram vector analysis.Intra-specific K2P genetic distance averaged 0.008±0.005 (0-0.035) for COI, and 0.005±0.010 (0-0.045) for 16S;inter-specific K2P genetic distance averaged 0.276±0.118 (0.102-0.557), and 0.366±0.190 (0.058-0.864) for COI and 16S,respectively.