Abstract: DNA Barcoding is a taxonomic technique that uses short genetic DNA sequence(s) for fast species identification and it has been among hot topics in modern taxonomy methods. In this study, the potential barcode sequences of 18 S rDNA, ITS and matK genes of seagrass samples（HCSD1、HCSD2、HCSD3） from Shuangdao Bay and Chudao of Weihai, Shandong, were cloned for phylogeny analysis. The results showed that the 18 S rDNA sequence was highly conserved. ITS and matK genes showed a higher degree of polymorphism than 18 S rDNA sequence and DNA taxonomy of matK sequence was consistent with morphological taxonomy. Samples HCSD1 and HCSD2 were identified as Z. marina, and samples HCSD3 was identified as Z. caespitosa. The results indicated that matK sequence is a good DNA barcode for seagrass delimitation in North Coastal of China.