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<i>Schizothorax kozlovi</i> is an endemic and vulnerable fish species found in the upper Yangtze River in China. Over the past few years, the population resources of <i>S. kozlovi</i> have been nearly completely depleted owing to multiple contributing threats. While the complete mitochondrial genomes serve as important molecular markers for phylogenetic and genetic studies, the mitochondrial genome of <i>S. kozlovi</i> has still received little attention. In this study, we analyzed the characterization of the mitochondrial genome of <i>S. kozlovi</i> and investigated the phylogenetic relationships of <i>Schizothorax</i>. The complete mitochondrial genome of <i>S. kozlovi</i> was 16,585 bp in length, which contained thirty-seven genes (thirteen protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), twenty-two transfer RNA genes (tRNAs)) and two non-coding regions for the origin of light strand (OL) and the control region (CR). There were nine overlapping regions and seventeen intergenic spacers regions in the mitochondrial genome. The genome also showed a bias towards A + T content (55.01%) and had a positive AT-skew (0.08) and a negative GC-skew (−0.20). All the PCGs employed the ATG or GTG as the start codon and TAA, TAG, or single T as the stop codon. Additionally, all of the tRNAs displayed a typical cloverleaf secondary structure, except trnS1 which lacked the D arm. The phylogenetic analysis, based on the maximum likelihood (ML) and Bayesian inference (BI) methods, revealed that the topologies of the phylogenetic tree divided the <i>Schizothorax</i> into four clades and did not support the classification of <i>Schizothorax</i> based on morphology. The phylogenetic status of <i>S. kozlovi</i> was closely related to that of <i>S. chongi</i>. The present study provides valuable genomic information for <i>S. kozlovi</i> and new insights in phylogenetic relationships of <i>Schizothorax</i>. These data could also offer fundamental references and guidelines for the management and conservation of <i>S. kozlovi</i> and other species of <i>Schizothorax</i>.