Molecular markers are providing valuable results on studies for the characterization of genetic variability, population structure and identification of myiasis-causing flies from Calliphoridae family. This family includes species of economic, forensic and medical importance. Forensic and population studies require precise identification, factor that can be hindered by morphological and ecological similarities, especially during the larval stage. For this study, the control region (CR), which is the major non-coding portion of the mtDNA, was sequenced for fifteen calliphorid species, recovered by two PCR reactions using specific and universal primers. The A domain of CR showed six conserved sequence blocks (CSBs) that might be related to functional activities, such as the transcription and replication of the mtDNA. The nucleotide content of this domain reaches 92.3% of A+T. Because of its CSBs, the A domain of the CR is a potential marker for phylogenetic reconstruction of recent diverged taxa. The B domain, however, exhibited hipervariability, with lengths varying from 650 to 1700 bp, limiting its utility for phylogenetic reconstruction, but that may be useful as a molecular marker for species identification. In addition, a complete duplication of the tRNA^Ile was found on five Chrysomya species studied. This duplication ranges from 112 to 123 bp, including the flanking regions of the tRNA^Ile. The duplication has an identical sequence when compared to the other tRNA^Ile gene, found in all Hexapoda. This duplication may be used for Chrysomya genus identification, since it has not been reported for other genus of Calliphoridae.