Abstract: Ponyfishes of genus Eubleekeria, order Perciformes, Leiognathidae family, are widely distributed in the Indo-West Pacific. They are small edible fish. Using molecular methods and morphological analysis, the taxonomy of genus Eubleekeria in coastal waters of China was discussed. We collected 153 specimens of ponyfish from four locations (Zhanjiang, Beihai, Fangchenggang and Dongxing) of Chinese coastal waters during 2014—2015. All individuals were identified as Eubleekeria jonesi (James, 1971). The diagnosis features were as follows: when mouth is closed, the lower orbital margin above horizontal line passed through the gape; the cheeks are exposed and the interspace of pelvic keels is naked; the dark blotch on the dorsal fin are dark gray; nape with a semicircular naked area. After re-examining the taxonomy books in mainland China, we found that the species identified as Leiognathus splendens or Eubleekeria splendens (Cuvier, 1829) may be E. jonesi. We also analyzed the COI sequences of E. jonesi and related species. The mean genetic distances by Kimura-2-parameter model within E. jonesi and E. splendens were 0.005 and 0.006, respectively; and the average genetic distance between E. jonesi and E. splendens was 0.130, which supports their separate species status. The results are consistent with the morphological method in this study.