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 phonetic 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.An obvious "barcoding gap" was detected for all species in both markers and all individuals of a species clustered together in both the CO1 and 16S trees.Further confirmatory evidence was also provided through indicator vector analysis.Meanwhile,both COI and 16S supported a new species as a separate species within genus Clytia,that was confirmed by detailed observation of medusa and polyps of this species.Hence,both COI and 16S appear to be accurate and efficient markers for hydromedusae identification in Taiwan Strait.Our results indicated that life cycle and DNA-based studies should be a standard approach in future biodiversity investigations of Hydromedusae species.