The taxonomic status of Episoriculus umbrinus has been contentious. This study aims to clarify its taxonomic position through mitochondrial genome analysis. Specimens of E. umbrinus were obtained from Liupanshui City, Guizhou Province, China. Genomic DNA was extracted, and 15 primer pairs were designed to amplify and sequence the complete mitochondrial genome of E. umbrinus. The results revealed that the mitochondrial genome of E. umbrinus is a circular double-stranded structure with a length of 17,073 bp, comprising 13 protein-coding genes, 1 control region, 22 tRNA genes, 2 rRNA genes, and 1 origin of L-strand replication. Compared with E. caudatus, differences were observed between the two species in terms of replication origins, gene overlap regions, base lengths, and termination codons. Genetic distance analysis of mitochondrial protein-coding genes showed that the genetic distance between E. umbrinus and E. caudatus ranged from 0.069 to 0.125. A phylogenetic tree constructed based on the concatenated sequences of the 13 protein-coding genes indicated that E. umbrinus clustered as a distinct branch with the other three species within the genus Episoriculus. This study confirmed at the molecular level that E. umbrinus is an independent species rather than a subspecies of E. caudatus. The mitochondrial genome sequence of E. umbrinus provides an important supplementary information for the genetic research of this species and offers new evidence for the phylogenetic study of the tribe Nectogalini.