Megaselia spiracularis and Dohrniphora cornuta were two forensically important flies in relatively sealed environments. Their mitochondrial genomes were first sequenced, annotated, and phylogenetic analyses were performed with other 8 species of the Asehiza in this study. Maximum-likelihood phylogenetic tree revealed that Phoridae is closer to Platypezidae and Lonchopteridae within Diptera. This work increases the databases of Phoridae species, and contributes to the further study of species identification and phylogenetics of this family.