[Objectives] To analyze the structure and characteristics of the mitochondrial genome of the genus Micromys and elucidate the phylogenetic relationships of this genus through mitochondrial genomic analysis, we conducted mitochondrial genome sequencing for M. minutus, M. erythrotis, and M. pygmaeus. [Methods] The mitochondrial genome structure, base composition, and codon usage were analyzed by SnapGene 6.0.2 and PhyloSuite 1.2.2. The secondary structure of tRNA was analyzed via the online tool tRNAscan-SE. On the basis of the concatenated sequences of 13 protein coding genes, the maximum likelihood and Bayesian inference phylogenetic trees were constructed in MEGA 11.0 and MrModeltest2 v2.4, respectively. [Results] The complete mitochondrial genome sequences of M. minutus, M. erythrotis, and M. pygmaeus obtained in this study were 16 239 bp, 16 240 bp, and 16 239 bp, respectively. Their structures all included 22 tRNA-encoding genes, 13 protein-coding genes, 2 rRNA-encoding genes, one origin of light strand replication (OL), and one control region D-loop. The codon usage patterns of M. minutus and M. pygmaeus were similar, while M. erythrotis showed great differences in codon usage from the other two species (Fig. 1). The 20 types of tRNA in the three species could form a cloverleaf secondary structure, while trnK and trnS1 could not fold into a cloverleaf structure due to the absence of D-loop and dihydrouridine arm. All mismatches in the tRNA secondary structures were U-G mismatches. The genetic distances across different parts of the mitochondrial genome indicated that M. minutus and M. pygmaeus had a smaller genetic distance (Table 1), and the phylogenetic tree also showed that the two species were in the same branch, indicating a closer phylogenetic relationship (Fig. 2). [Conclusion] The mitochondrial genome structure and characteristics of the three species of Micromys in this study are consistent with those of vertebrates. The analysis of the mitochondrial genome revealed that M. minutus and M. pygmaeus have a closer kinship, while M. erythrotis is distant from the other two species.