The large yellow croaker (), mainly distributed in coastal waters of China and East Asia, is one of the most important economic marine fish in China, and represents the largest yield for a single species in Chinese marine net-cage farming. Nevertheless, because of exhaustive fishing, habitat degradation and high-density aquaculture, the genetic diversity of the species is at a low level, and mariculture of the species is facing serious challenges from germplasm degeneration and susceptibility to infectious disease agents. Studies of the large yellow croaker have focused on the comparison of genetic differences among culture populations, and few of them have reported on comparative analysis among a wide range of wild and cultured stocks. To study the genetic diversity of wild and cultivated populations, we amplified and sequenced the mitochondrial cytochrome oxidase I () gene of 336 samples from eight wild populations and six cultivated populations. The amplified fragment was 621 bp, containing a total of 38 mutation sites which included 23 parsimony-informative sites and 15 singleton mutation sites. The results showed that the wild populations contained 38 mutation sites, accounting for 100% of the total variations, while the cultivated populations contained 8 mutation sites accounting for 21.05%. We also detected 34 haplotypes in all 14 groups, and these were characterized by high haplotype diversity (0.587) and low nucleotide diversity (0.00194). The haplotype diversity index of the wild and cultivated populations ranged from 0.714 to 0.952 and from 0.000 to 0.581, respectively. The coefficient of gene differentiation () between wild and cultured groups was 0.04982, accounting for 4.98% of the total variance. There was an extremely significant difference (>0.05), and accounting for 93.56% within populations (<0.01). Analysis of AMOVA and phylogenetic trees revealed that the genetic diversity of the large yellow croaker was in lower level, and that the genetic diversity in cultivated populations was significantly lower than that in wild populations. In addition, the variation within populations contributed its major genetic variation, and there was extremely high genetic differentiation between wild and cultivated groups but not significant within populations. The large yellow croaker from the East China Sea and Yellow Sea should belong to the same geographic population, but there is still a low level of genetic differentiation among the two groups, the genetic diversity of Yellow Sea groups being higher than that of the East China Sea. This study can provide a theoretical basis for resource conservation and germplasm recovery.