Xenophysogobio boulengeri is an endemic fish to mainstream and most tributaries of the upper Yangtze River. The complete mitochondrial genome sequence of X. boulengeri has been amplified and sequenced. The mitochondrial genome sequence was 16,611 bp, and the gene order and contents were identical with that of other previously reported fish with 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes, and a non-coding control region. Most of genes were encoded by Heavy-Strand (H-strand), except 8 tRNA and ND6 genes, which were encoded by Light-Strand (L-strand). Base composition of the genome was A (30.8%), T (27.0%), C (25.8%) and G (16.4%) with an A+T rich feature as that of other vertebrate mitochondrial genomes.