PURPOSE: Hypoderma pantholopsum is a parasite that parasitizes Tibetan antelopes (Pantholops hodgsonii). This study aims was to reveal the genetic diversity within H. pantholopsum and contribute to the protection of Tibetan antelope. METHODS: H. pantholopsum was subjected to mitochondrial genome sequencing, annotation, and phylogenetic analysis. PhyloSuite and BEAST were used to construct phylogenetic tree and divergence time for the parasite. RESULTS: The complete H. pantholopsum genome was 16,265 bp in length. The complete mitochondrial genomes contained 37 typical genes, which included 13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs. Phylogenetic trees constructed based on the 18S rRNA, 28S rRNA, and mitochondrial genome sequences showed that H. pantholopsum clustered on the same branch as the Hypoderma species in the GenBank database. According to the divergence time for the COI gene, H. pantholopsum emerged and differentiated approximately 11.59 million years ago (Mya), which indicates that H. pantholopsum appeared much earlier than H. bovis and H. sinense in the genus Hypoderma. CONCLUSION: The present study explored that the complete mitochondrial genome of H. pantholopsum, along with the phylogenetic evolution, and divergence time estimation, provide valuable data for future investigations into the phylogeny and differentiation of Hypoderma species on the Qinghai-Tibetan Plateau.