Background: The phylogenetic resolution within the Gloydius halys-intermedius Complex remains debatable due to the following reasons: loci selection in previous studies varied between authors; limited dataset (1−5 mitochondrial or nuclear gene fragments); lack of sampling density; and nodal supports at specific nodes remain weak, specifically within Gloydius cognatus, G. halys, and G. stejnegeri. Objectives: To revise the taxonomic and phylogenetic relationships within the G. halys-intermedius Complex, we reconstructed the molecular phylogeny and performed species delimitation based on the complete mitochondrial genomes. Methods: In this study, twelve nomenclatural groups of Gloydius species were involved in the computation of Bayesian phylogenomic inference, five of the twelve nomenclature groups were newly sequenced, while the rest were acquired from the National Center for Biotechnology Information (NCBI). The Bayesian phylogenomic inference was constructed based on 13 mitochondrial protein-coding genes. Species delimitation was performed by two distance-based methods (ABGD and ASAP) and two tree-based methods (GMYC and bPTP). Results: This research resolved the systematic relationship within the G. intermedius Complex with the support of mitogenome-based phylogenomics, while indicating cryptic diversity within the Gloydius halys-intermedius Complex: G. intermedius samples from South Korea show as paraphyletic to the cluster of the samples from northeastern China. Species delimitation results based on four models resemble each other, supporting Gloydius caucasicus, G. cognatus, G. halys, and G. stejnegeri, each representing full species. The species delimitation results of this research also resemble the nomenclatural species based on previous morphometrical results. This research indicates that species delimitation efforts based on the phylogenomic approach would likely resolve complex evolutionary relationships.