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Acerina cernua is a specific percid species that naturally occurs in Xinjiang Irtysh River basin, China. The complete mitochondrial genome of the ruffe A. cernua was first determined (Accession number MK509809), with a total length of 16,677 nucleotides, of which 15,579 nucleotides are coding DNA, and 1098 nucleotides are non-coding DNA. It has the common feature with those of other fishes with respect to genome structure and gene arrangement. It contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region (D-loop region). The complete mitochondrial genome of ruffe A. cernua provides an important data set for further study on its classification.