In this study, the mitogenomes of four smelts (Hypomesus nipponensis) were sequenced and the genomic variation and phylogeny were examined. The mitogenome consisted of 16,782 bp and showed 99.5 99.7% sequence similarity with the previously released sequence. A total of 130 single nucleotide polymorphisms were detected and they were present in 2 rRNA genes, 6 tRNA genes, 12 proteincoding genes, and 1 non-coding region. This study provides important information for the classification of H. nipponensis and related species.