The phylogenetic relationships between the subgenera and/or species of genus Apodemus are controversial and problematic. In this context, complete mitogenome analyses, along with Cytochrome b and Cytochrome oxidase I data, were performed to elucidate the phylogeny of this genus. The complete mitochondrial genome characteristics of four species (Apodemus mystacinus, Apodemus uralensis, Apodemus ponticus, and Apodemus witherbyi) were reported for the first time, and mean genetic distance (d) and Bayesian Inference (BI) trees were provided. Accordingly, Sylvaemus, Karstomys, Apodemus, and Alsoyms subgenera were separated by high d values and hypothesised to be different genera. In terms of Sylvaemus species, mitogenome analyses gave more statistically reliable results, with Syl. flavicollis/ Syl. ponticus being closer to Syl. uralensis, while Syl. witherbyi was closer to these species than A. sylvaticus. In addition, the results of the analyses support the idea that Syl. ponticus is a distinct species from Syl. flavicollis.