In order to assess the power of DNA-based metabarcoding in the monitoring of marine biodiversity, we ultilized both metabarcoding technique and morphological method to compare communtiy diverstiy of copepods, which were collected from 22 sites along the Yalvjiang Estuary of China. The results showed that: (1) a total of four order, 23 family, 32 genus and 229 operational taxonomic units (OTUs) were detected through the metabarcoding technique, whereas only three order, five familiy, five genus and six species were identified based on the morphological method. In addition, most taxonomic categories (100% order, 80% family, and 80% genus) identified based on the morphological method could be also detected using the metabarcoding technique. Reversly, however most taxonomic categories (25% order, 83% family and 88% genus) detected using the the metbarcoding technique could not be identified based on the morphological method. The results suggested that the metabarcoding technique was more powerful than the morphological method in the assessment of copepod diversity. (2) The variation of diversity index based on the metabarcoding method was significantly consistent with the morphological method (r=0.542, P=0.024), suggesting good comparability between the two methods. Our results indicated that the DNA-based metabarcoding technique had high application potential in efficient assessment of marine biodivesity.