Marine biodiversity is an important indicator of ecosystem health and the material basis for the development and utilization of marine biological resources. Shandong coastal waters are the main breeding grounds for Bohai and Yellow Sea fisheries resources. These waters provide a wealth of biological resources and a superior fisheries habitat for China, Japan, South Korea, and North Korea. However, the Shandong offshore fisheries resources have been trending downward in recent years, and species abundance and diversity have decreased. Therefore, identifying and classifying the fish species in these coastal waters are urgently required to effectively protect and use these resources. In this study, 229 DNA sequences of the cytochrome oxidase subunit I (I) gene from 77 common marine fish species in 13 orders, 50 families, and 73 genera from offshore of Shandong were analyzed to test the efficacy of species identification using a DNA barcode microarray. The results showed that interspecific genetic distance was larger than intraspecific distance. All 77 sequences formed species units in a neighbor-joining dendrogram, indicating that DNA barcodes can be used to identify these 77 species. Sixty-four specific probes were screened to identify the corresponding species among the 77 species based on the I genes and accounted for 83.1%. Thus, the DNA barcode microarray provided technical support and a new way to identify fish species in the coastal waters offshore of Shandong.