Gymnodiptychus integrigymnatus is a small endemic fish species found in southwest China. This study aimed to investigate the phylogenetic relationships and mitogenomic characteristics of G. integrigymnatus. The complete mitochondrial genome of one individual of G. integrigymnatus was sequenced using the Illumina HiSeq X Ten sequencing platform and comprehensively characterized. The mitochondrial genome was 16,714 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a typical control region. The genome composition showed a positive A + T skew (0.029) and a negative G + C skew (−0.198). All tRNAs were predicted to form typical cloverleaf secondary structures, except for tRNA-Ser (GCT), which lacked the DHU stem. Phylogenetic reconstruction based on 13 PCGs revealed that the subfamily Schizothoracinae was not a monophyletic group. Two major clades were identified within this subfamily: one comprising primitive taxa (Percocypris, Aspiorhynchus, and Schizothorax) and the other consisting of specialized and highly specialized groups. Gymnodiptychus integrigymnatus was distinct from both its congeners and the specialized clade and was instead recovered within a highly specialized group of the Schizothoracinae subfamily. This study offers novel perspectives on the taxonomy and phylogenetic relationships within the Schizothoracinae subfamily, with a specific focus on G. integrigymnatus, thereby enhancing the understanding of the systematics and phylogeny of the Schizothoracinae subfamily.