Abstract: At present, there is still a lack of research on the germplasm resources of the moray eel genus Gymnothorax in the world, and its taxonomic classification and resource documentation require urgent revision and updating. In this study, we collected and identified a Gymnothorax specimen from Zhanjiang, Guangdong Province through morphological and molecular biological methods, so as to provide a scientific basis for the germplasm resource analysis and species catalog updating of this genus. The specimen was analyzed for external morphological characteristics and its complete mitochondrial genome was sequenced. The morphological results show that the specimen exhibited a uniform brown body coloration without patterns or spots, a high dorsal fin originating anterior to the gill opening, light grayish edges on all fins, a slightly arched lower jaw preventing complete mouth closure, uniserial teeth, and a vertebral formula of 5-58-140. These characteristics aligned closely with the newly described species G. poikilospilus sp. nov. The complete mitogenome was 16,572 bp in length, comprising 22 tRNA genes, 2 rRNA genes, 13 protein-coding genes, and 1 non-coding control region, with gene order and content conserved among teleosts. Phylogenetic analysis based on 12 protein-coding genes reveals that G. poikilospilus clustered closely with G. odishi, G. reevesii and G. pseudothyrsoideus. In the COI-based phylogeny, the studied specimen formed a monophyletic clade with G. poikilospilus. Genetic distance between the two species was only 0.004, far below the species delimitation threshold of 0.020, further confirming their conspecificity. This study represents the first record of G. poikilospilus in mainland China, integrating morphological and molecular evidence to expand the germplasm resource database and facilitate future taxonomic research on Gymnothorax.