Murinae is the largest known subfamily of Muridae and includes 15 tribes and 3 genera (incertae sedis). Although the phylogeny of Murinae has been studied, its phylogenetic relationships have not been completely elucidated. We used phylogenetic framework and molecular dating methodologies with the vast majority of available mitochondrial genomes to disentangle the phylogenetic relationships and evolutionary history of Murinae. Sixteen tribes were identified within the Murinae subfamily. Among these, fifteen tribes were found to be consistent with those currently recognized. Hapalomyini (Clade A) was located at the base of the Murinae clade with strong nodal support contrary to previous studies, which showed that Phloeomyini diverged first. The Clade B consisted of Micromyini, Rattini, and the genus Vernaya. Vernaya cannot be accommodated in any existing tribe. The origin of Murinae dates back to 17.22 Ma. The split between Micromyini and Vernayini was dated to 11.69 Ma during the Miocene, indicating that they were both early branches of Murinae. Combined with the differences between Vernaya and its sister tribes (Micromyini and Rattini) in morphology, skull and teeth, we validated a new tribe, Vernayini tribe nov. We believe that it is necessary to combine morphological and molecular perspectives (especially from a genome-wide perspective) to determine the phylogenetic position of tribes with an uncertain taxonomic position in Murinae.