Abstract: Of seaweeds from Gracilariales, Hypnea produces kappa carrageenan, and Gracilaria and Gracilariopsis produce agar, both of which have important commercial value. This study provides morphological descriptions and DNA barcoding analysis of several red algae isolates from Dongshan Bay, Fujian Province. Based on the DNA barcode marker COI (Cytochrome Oxidase I) and rbcL gene, they are Hypnea flexicaulis, Gracilaria vermiculophylla and Gracilariopsis lemaneiformis. The genetic diversity analyses based on the COI gene showed that three different haplotypes of H. flexicaulis were identified. Two of them were never reported before, and the third on was the shared haplotype with samples from Taiwan and Jeju Island, with corresponding morphological differences. The Gracilaria vermiculophylla samples from Dongshan Bay belong to the late-branching haplotype of the COI gene sequences, which evolved later than other haplotypes that distributed in the northwest Pacific. Four samples of Gracilariopsis lemaneiformis from Dongshan Bay have the same sequences as those of northern cultivated strains. This study preliminarily revealed the rich diversity of Gigartinales red algae in the intertidal zone of Dongshan Bay, providing basic data for the development and utilization of algal resources in this region.