In this study, genetic diversity and population genetic structure of Sagitta enflata in the northern South China Sea were investigated by 623 bp fragment of mtDNA COI gene sequence. A total of 146 individuals were collected from nine stations and 92 different haplotypes were obtained. 485 variable sites (210 were parsimony informative and 275 were singleton variable sites), and no insertion or deletion was found. An analysis of molecular variance (AMOVA) and conventional population statistics (F-ST) revealed a low level of genetic differentiation among nine populations (F-ST = 0.14794, p < .05), indicating no geographical patterning among nine populations. The present results were able to provide a reference for the phylogenetic relationships and assessment of the genetic structure of S. enflata in the northern South China Sea
