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The inconsistency between traditional morphological taxonomy and molecular phylogenetic data is a major issue that puzzles the study of fish classification and evolution. Although mitochondrial genes are commonly used in phylogenetic analyses to compare fish species, the mitochondrial evolution and diversity of <i>Schistura</i> are still not well understood. To better understand the evolution of <i>Schistura</i>, we sequenced the mitochondrial genome of <i>Schistura fasciolata</i> and compared it with other species of <i>Schistura</i>. A 16,588 bp circular mitochondrial genome of S. fasciolata was obtained and it contains 13 protein-coding, 22 transfer RNA, and two ribosomal RNA genes, and a non-coding control region. The gene arrangement in the mitochondrial genomes of all <i>Schistura</i> species was consistent. However, we also found that <i>S. fasciolata</i> was not monophyletic. Although mitochondrial genes can be effectively used for <i>Schistura</i> species identification, they may not be suitable for inferring the evolutionary process of <i>Schistura</i> species. These results provide support for the use of mitochondrial genes in identifying <i>Schistura</i> species, and also serve as a warning against mistakenly using them to evaluate the evolution process of <i>Schistura</i> species.