Due to extensive morphological plasticity, the taxonomy of Cladophora species remains unclear. As one of the widely distributed species, C. gracilis was reported to hold many varieties, which make it difficult to identify the species. This study explored the morphology diversity of nine C. gracilis samples collected along the coast of western Yellow Sea. Some samples showed extremely varied characteristics, by which one cannot classify them correctly. Hence, 18S rDNA and nuclear ribosomal DNA internal transcribed spacer regions (ITS) sequences were employed to delimit species. For 18S rDNA, sequence similarity ranged from 99.6％ to 100％. For ITS region, the similarity ranged from 98.7％ to 100％. Molecular data strongly suggested that the morphologically heterogeneous samples were actually the same species. Characteristics comparison of the samples revealed that the taxonomy criteria including branching pattern and density, thallus color, height and texture varied widely, influenced by environmental conditions and age of alga. Besides, cell dimensions, as the relatively stable criterion, also exhibited intraspecific variance. Successful application of 18S rDNA and ITS sequences indicated that molecular method can be a powerful assistant as DNA barcodes to traditional morphology taxonomy.