<p>Mitochondrial DNA (mtDNA) is widely investigated in population genetics studies, which can provide valuable genetic information for marine fishery management. The control region (CR) is the most variable region in vertebrate mitogenomes, serving as a popular marker in population genetics studies of marine fish species. However, low CR variability in the Japanese anchovy (<i>Engraulis japonicus</i>) was found unexpectedly in this study, for which we newly assembled a mitogenome of the Japanese anchovy and conducted comparative analyses to examine the mitochondrial variation pattern of this species. Phylogenetic analysis revealed relatively long sub-branches between our assembly and the mitogenomes of <i>E. japonicus</i>, suggesting high-level intraspecific variation. Further comparative analyses identified a total of 184 variable sites, most of them (157/184, 85.33%) were located in protein-coding genes, with 20 sites in the CR. For variations in protein-coding genes, only two sites were categorized as non-synonymous substitution, indicating purifying selection. In addition, we also observed that the variation rate of CR was relatively lower than those of some protein-coding genes. Therefore, relatively low CR variability of the Japanese anchovy was detected in terms of the number of variable sites and variation rate. To the best of our knowledge, this should be the first report to uncover low CR variability in an abundant marine teleost species. We suggest that in population genetic studies, the diverse types of genetic markers shall be included to provide accurate genetic information for fishery management and conservation.</p>