Dramatically intensified economic development in the coastal areas of Zhejiang, China, has posed unprecedented challenges and pressures on the native coastal marine biota. Mugilids (Teleostei: Mugiliformes) are widely distributed across marine, brackish, and freshwater habitats in tropical, subtropical, and temperate regions of the world. In this study, DNA sequences of a consensus length of 611 nucleotides in mitochondrial Cytochrome c Oxidase subunit I (COI) were used to identify 144 mugilid samples collected from various intertidal waters along the coast of Zhejiang in the East China Sea. A total of 35 distinctive COI haplotypes was scored. Results of neighbor-joining (NJ) clustering clearly support classification of seven species, in agreement with morphological diagnosis: Planiliza affinis, Planiliza haematocheila, Planiliza sp. H, Planiliza subviridis, Crenimugil sp. A, Osteomugil cunnesius, and Mugil sp. C. Planiliza affinis was found to be the dominant mugilid in the coastal waters. This research provides critical scientific data for understanding the identity and abundance of mugilids and managing their fishery resources and habitats along the coast of Zhejiang.