The complete mitochondrial genome of Sinocyclocheilus anatirostris, which is an endemic cave fish species in the Youping Town, Leye County, Guangxi Province of China Belongs to the Hongshui River system, was reported for the first time. Phylogenetic analysis indicated that S. anatirostris was close to S. furcodorsalis,S. anatirostris diverged from S. furcodorsalis at about 6.07 Ma (90% HPD: (3.62,9.2Ma).The complete mitogenome of S. anatirostris was 16,577 base pairs (bp) and consisted of one control region, 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. The base composition of the mitogenome was 31.2% A, 24.45% T, 16.7% G, and 27.7% C, with overall 44.4% GC content. To better understand the diverse characteristics of the S. angularis group and provide clues about genetic adaptation,We sequenced the mitochondrial genes of Sinocyclocheilus anatirostris.