The structure and evolution of the mtDNA control region (CR) and its flanking genes in economically important dipterans from the family Muscidae (Brachycera: Calyptratae), Haematobia irritans, Musca domestica, Atherigona orientalis, and Stomoxys calcitrans are presented in this paper, along with the description of short noncoding intergenic regions possibly related to CR flanking sequences in Stomoxys calcitrans and Ophyra aenescens mtDNAs (ScIR and OaIR, respectively). S. calcitrans showed a large CR with an approximately 550-bp element tandemly repeated and a duplicated tRNA(Ile) gene. The characterization of H. irritans, M. domestica, A. orientalis, and S. calcitrans CR sequences led to the identification of seven conserved sequence blocks homologous to the elements previously described for Calliphoridae and Oestridae species (Brachycera: Calyptratae). Comparative analysis with Drosophila species (Brachycera: Acalyptratae) revealed four conserved regions. The putative functional roles of the conserved elements in the regulation of replication and transcription processes are addressed. The characterization of the structural organization of the mitochondrial genome CR demonstrates the plasticity of the mtDNA molecule in family Muscidae.64519-27