[Objectives] The study aims to analyze the complete sequence of the mitochondrial genome of Heizensteinia microcephalus and Chuanchia labiosa, and to explore the phylogenetic relationship of Schizothoracinae fishes based on the mitochondrial genome sequence. [Methods] We obtained the mitochondrial genome sequences of H. microcephalus and C. labiosa from NCBI and used the online software MitoAnnotator to map the mitochondrial genomes. The base composition of the whole mitochondrial genomes of both species was calculated using the Sequence Manipulation Toolbox. Relative synonymous codon usage(RSCU) was calculated using CodonW software. Ka/Ks values were calculated using KaKs_calculator v 3.0 software based on the NG method. The best nucleotide substitution model was automatically selected using the MFP parameter in IQtree2 software, and the maximum likelihood(ML) tree was constructed using the GTR + F + I + I + R2 evolutionary model, and the confidence value of each branch node of the phylogenetic tree was examined using bootstrapping with1 000 repetitions. Differentiation times were estimated using the MCMCtree subroutine in the PAML v4.9j package. [Results] The two mitogenomes are typical circular molecules of 16 726 and 16 705 bp in length containing 13 protein-coding genes(PCGs), 22 transfer RNA genes(tRNAs), two ribosomal RNA genes(rRNAs) and one non-coding control region(D-loop) (Fig. 1 and Table 2). In addition, the ATPase8gene showed a higher Ka/Ks value (0.527 and 0.256) and the NDL4gene showed a lower Ka/Ks value (0.527 and 0.256, Fig. 3). Maximum likelihood phylogenetic analyses revealed that H. microcephalus and C. labiosa were the closest relatives, and the genus Heizensteinia and the genus Chuanchia were closest to the genus Schizopygopsis (Fig. 4). The divergence between H. microcephalus and C. labiosa was dated back to 0.83 million years ago(Mya) (Fig. 5). [Conclusion] This study helped to improve biodiversity conservation strategies for highland fishes in the future.