“Hao Gen” is a common name for a small fish inhabiting the tidal flat of Jiaozhou Bay of the Yellow Sea. It is a target catch of a traditional subsistence fishery in Qingdao (Shandong, China), focusing on a single fish species, and is a famous specialty seafood of Jiaozhou Bay. However, the taxonomic classification and scientific name of “Hao Gen” have long been unclear. Recently, the catch of “Hao Gen” has continuously declined, indicating that its resources may be under threat. In this study, taxonomic identification using morphological methods and DNA barcoding technology was conducted to clarify the species identification and distribution information of “Hao Gen”. Ten “Hao Gen” fish samples were collected from a traditional fishing area of the tidal flat in the northern part of Jiaozhou Bay in April 2023. In the morphological study, seven countable traits (spine and ray numbers of dorsal fin and anal fin, pectoral fin ray numbers, longitudinal scales, rows of scales, scales before dorsal fin, and vertebrae numbers) and eight measurable characteristics (body length, body depth, head length, snout length, eye diameter, interorbital space, and caudal peduncle length and height) were selected and used for the quantitative analysis of samples. By comparing with historical literature records, the species was preliminarily identified as Acanthogobius elongatus (Fang, 1942). We examined the DNA barcode fragment with 542 bp of the mitochondrial cytochrome c oxidase subunit Ⅰ (COⅠ) gene of all samples. Six haplotypes were obtained, and all sequences were submitted to the GenBank database (Accession numbers: PQ407566–PQ407571). BLAST searches were performed to identify similar sequences in the GenBank. The comparative analysis and species identification also included homologous sequences from closely related species. Phylogenetic relationships among eight species of the family Gobiidae were reconstructed by MEGA Ⅹ using the maximum likelihood (ML) method based on the best-selected model Jukes-Cantor. The net genetic distance was calculated based on the Kimura 2-parameter (K2P) model. The results indicated that all DNA barcode sequences of the “Hao Gen” samples showed a high degree of similarity to the homologous sequences of the species A. elongatus, and the genetic distance between them was at the intraspecific level. In the phylogenetic tree, all the “Hao Gen” samples clustered with DNA barcode sequences of A. elongatus, published in GenBank. The results of morphological and DNA barcoding analysis were consistent, indicating that the “Hao Gen” samples could be identified as A. elongatus. According to the literature, the species of A. elongatus is distributed along the coast from Liaoning to Zhejiang in China, as well as the west coast of the Korean Peninsula, and it often inhabits the brackish waters of river estuaries. The species is classified as vulnerable and included in the “China Red List of Species”. In this study, the effective identification of “Hao Gen” fish and the first record of A. elongatus in Jiaozhou Bay address the long-standing issue of limited scientific understanding of the subsistence fishery catch species. These findings enhance the knowledge of fish diversity in Jiaozhou Bay and provide a scientific basis for the conservation of fishery resources and improving fisheries management in the area.