<i><i>Mastophorus</i> muris</i> is a prevalent nematode parasite of rodents that can cause pathogenic manifestations or mortality. As the only 1 species in the genus <i>Mastophorus</i> and the sole member of the family Spirocercidae, its biology, molecular identification, and population genetic structure remain poorly studied. In this study, the complete mitochondrial genome of <i>M. muris</i> was fully assembled and annotated through high-fidelity next-generation sequencing for the first time, to resolve its molecular architecture with nucleotide-level precision. The 13,668 bp mitogenome encodes 36 genes, including 12 protein-coding genes (PCGs), 22 transfer RNAs, and 2 ribosomal RNAs (s-rRNA and l-rRNA). The 10,384 bp PCGs account for 76.0% of the mitogenome, with AT (71.7%) and GC (28.3%) contents, AT skew (-0.494) and GC skew (0.477), indicating pronounced nucleotide bias. Analysis of 12 PCGs revealed that TTG, ATT, ATA, or GTG were the common start codons. TAA was the predominant termination codon, while some PCGs (<i>cob, nad1</i>, and <i>nad3</i>) were deduced to end with an incomplete codon T. T-rich codons such as TTT-Phe (16.3%), TTG-Leu (8.5%), GTT-Val (6.7%), ATT-Ile (6.3%), TAT-Tyr (5.6%), TTA-Leu (4.6%), and TCT-Ser (4.3%) were used more frequently. Phylogenetic analysis using the concatenated nucleotide sequences of 12 PCGs, and the NJ tree analysis results showed that <i>M. muris</i> was more closely related to the genus <i>Gongylonema</i>, which indicated that the family Spirocercidae was more closely associated with <i>Gongylonema</i>tidae. This study provides valuable mitogenomic data for nematode phylogeny, diagnostics, population genetics, and comparative mitogenomics.