The mitochondrial DNA (mtDNA) is a circular genome with maternal inheritance, which generally contains 37 genes and a control region. Because of the extensive use of the mtDNA as a molecular marker in evolutionary studies, its complete sequencing has been extremely impelled in the last few years. The Calliphoridae (Diptera: Brachycera) family has a veterinary, economic and forensic importance since is constituted by myiasis-causing flies. Until now, 45 Calliphoridae species are listed in GenBank, including two complete mitochondrial genomes of the species Cochliomyia hominivorax and Chrysomya chloropyga. Through the long-PCR technique, it is possible to amplify the whole mitochondrial genome in few fragments. This approach can provide the attainment of sufficient DNA for shotgun of amplified fragments. The amplification and sequencing of the mtDNA of Chloroprocta idioidea, Mesembrinella bicolor and Phormia regina, associated to the sequenced mtDNA on GenBank will provide a comparison of the nucleotide content, skewness, aminoacid sequences, and codon usage among the mtDNA of Calliphoridae species and dipteran species. Until now, the cox1 gene is the most used molecular marker for studies among Calliphoridae and across a broad range of insects, but the comparison of individual and concatenated sequences of another mitochondrial genes among dipteran species have shown distinct degrees of conservation, indicating that some of them also should be employed as reliable molecular markers. The complete mitochondrial genomes are a useful source for improving primer designing, molecular identification of species, and for elucidating the potential of individual and combined genes for molecular systematic studies of Diptera.