The goby is a key link in the food chain at the bottom of the ocean and plays an important role in the material circulation and energy flow of the ecosystem. Due to the large variety, extensive distribution, and small size of the goby, as well as different degrees of degradation and specialization in morphology, it presents great challenges to morphological classification and identification. In this study, 73 adult and juvenile goby samples from the Yellow Sea and Bohai Sea were identified by morphology and DNA barcoding. According to the morphological classification, 12 species of 9 genera were identified, while 13 species were identified belonging to 10 genera of family Gobiidae. Thus, in the case of insufficient experience in morphological identification or unclear morphological characteristics of juvenile fish, DNA barcoding can effectively identify species. At the same time, the list of recorded species of family Gobiidae in the Bohai Sea and Yellow Sea of China was systematically sorted out, with a total of 47 species of 29 genera. According to the recorded species list, the DNA barcodes of 29 species of 18 genera belonging to the family Gobiidae were screened and downloaded from the BOLD and NCBI databases. Combined with the 13 species of 10 genera of gobies identified in this study, a phylogenetic tree of 42 species of 26 genera was constructed, covering 89.36% of the recorded species of gobies in the Bohai Sea and Yellow Sea of China. The DNA barcode classification system of gobies was established by confirming and revising the molecular phylogenetic relationship and morphological classification status of gobies. The results of this study demonstrate the recognition efficiency of DNA barcoding in the classification of the gobies, make up for the shortcomings and limitations of traditional morphological identification methods, enrich the goby DNA barcode database, improve the goby DNA barcoding classification system, and provide a scientific basis for research on the conservation biology, evolutionary biology, and biogeography of goby fish.