Larimichthys crocea, an economically important fish species along the coast of China, has faced severe threats to its resources in recent years due to overfishing and loss of genetic diversity. To characterize the phenotypic traits of the less-studied Naozhou group of L. crocea, a combination of fish morphology, otolith morphology, and otolith chemistry was employed to discriminate the two stocks of L. crocea, the Naozhou and Min-yuedong groups sampled in Zhanjiang and Zhangzhou, respectively. The results of the principal component analysis indicated that the two populations could not be separated by the first two principal components of fish morphology, but could be distinctly separated by otolith morphology. Analysis of variance (ANOVA) indicated significant differences in fish and otolith morphologies between the two stocks (P＜0.05). The deformation diagram of fish morphology showed that Naozhou individuals were generally more elongated, with relatively shorter pectoral fin bases than Min-Yuedong individuals (P＜0.05). A deformation diagram of otolith morphology revealed that the otoliths of the Naozhou stock were more compressed overall, exhibiting a thicker neck in the sulcus and a relatively deeper first posterior dorsal depression than those of the Min-Yuedong stock (P＜0.001). Otolith chemical analysis revealed that the Ba/Ca and Sr/Ca ratios in the otoliths of the Naozhou stock were significantly higher than those in the Min-Yuedong stock, whereas the Mn/Ca ratio was significantly lower (P＜0.0001). There were no significant differences in the Mg/Ca ratios (P＞0.05). The Sr/Ca ratios exhibited the most pronounced differences between the two stocks from the core to the edge of the otolith when compared to the ratios of Ba, Mg, and Mn with Ca, with virtually no overlap at the measurement points. Discriminant analysis results indicated that the discrimination accuracy based on fish morphology (85.2%) was lower than that based on otolith morphology (100%) and chemistry (100%). The morphological differences between the two groups may be related to the differences in water flow and temperature between their habitats, with the Naozhou group inhabiting lower-flow and higher-temperature environments. Variations in otolith chemistry can be partly explained by salinity and temperature. Fish morphology, otolith morphology, and microchemical analyses demonstrated sufficient efficacy in the stock identification of the Naozhou and Min-yuedong groups of L. crocea. These findings provide a scientific basis for stock discrimination and fishery management of L. crocea.