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In this study, we first determined the complete mitochondrial genome of Erromyzon sinensis. It was 16,560 bp in length and contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, a light strand origin of replication (OL), and a control region (D-loop). In addition, its overall nucleotide composition was 29.4% of A, 16.8% of G, 25.7% of T, and 28.1% of C, with a total of 55.1% A + T content. Phylogenetic analysis based on 13 protein-coding genes revealed that E. sinensis had the closest relationship with E. kalotaenia. Our study aimed at providing basic information for molecular systematics and conservation genetics research of E. sinensis.