Conger myriaster is a commercially important species in China. The population structure of C. myriaster remains a mystery and the spawning activities of C. myriaster are not well known because larvae and adults of this species have separate habitats and its spawning grounds have not been discovered. Several hypotheses on the population structure and spawning grounds of C. myriaster have been proposed. Takai described that this species has a single population with a single spawning site. On the other hand, there are also some indications of the possibility of multiple spawning populations. So it is important to clarify the population structure of C. myriaster to provide basics for future detailed examination on its life history. If this species has multiple populations, there may be some morphological and genetic differences in the samples collected from different sea areas at the same time. In the present study, we combined morphological and genetic methods to understand the morphological and genetic differences of C. myriaster in the two different localities of Zhoushan (East China Sea) and Qingdao (Yellow Sea). The morphological studies were conducted by using one-way ANOVA, discriminant analysis and principal component analysis. Genetic analysis of the mitochondrial DNA (mtDNA) sequence was carried out. Results from morphological studies indicated that there were intermuscular bones of "I" type in the muscle of the C. myriaster from Zhoushan group but not in Qingdao group. The results of multivariate statistical analysis showed that there were significant differences in seven morphological measurements (preanal length, head width, snout length, rictus length, eye diameter, predorsal length) of C. myriaster from different groups, and these measurements were all over the body. In principal component analysis, C. myriaster from different groups could be distinguished by a scatter plot based on the first two principal components. Discriminant analysis results showed that the correct diserimi-nation rates of Qingdao and Zhoushan groups were 100% and 94.7%, respectively. The results of multivariate statistical analysis methods showed that there were significant differences in morphology between the two groups. But according to the Mayr's 75% rule, most differences in morphology between the two groups were characterized under-subspecies. Genetic results suggested that there was no significant difference in genetic diversity between samples collected from different locations on the level of mtDNA. The neighbor-joining tree showed no genealogical clade. The pairwise fixation index F_ST revealed no significant genetic difference between the two groups. The present study provides morphological and genetic basis for the taxonomic status of the C. myriaster population in China. It also provides useful information for the population assessment, management and conservation of C. myriaster.