To identify the fish eggs which were obtained from Enteromorpha algae of Rudong sea area, DNA barcoding technique was used. Our result showed there were no variable sites in mtDNA COI gene sequences among our fish eggs, larvae, adults and Japanese halfbeak (Hyporhamphus sajori), and the genetic distance among them was 0. However, there are high variable sites among the eggs, larvae, adults and the other Beloniformes fishes, and the genetic distance among them is 21.9%-26.4%. The Neighbor-joining (NJ) phylogenetic tree also indicated that the eggs, larvae, adults and the Japanese halfbeak formed a monophyletic group. Therefore, it is suggested that the fish eggs which we obtained from Enteromorpha algae of Rudong sea area were Hyporhamphus sajori. Based on our identification result, we further discussed the reasons of Japanese halfbeak spawning in algae and how to use this phenomenon to recover the offshore fish resources.