Analysis of the animal mitochondrial DNA (mtDNA) provided useful molecular markers for evolutionary studies. Features such as gene content and gene order used to be conserved in the animal mitochondrial genome, however, the occurrence of rearrangements in the mtDNA, specifically regarding the position of  tRNAs genes, has been frequently reported in an increasing number of arthropod species. The characterization of mtDNA gene orders could contribute for understanding the diverse patterns of molecular evolution of this genome and, in addition, provide a potential informative tool for phylogenetic analysis. This work reports the sequence analysis of three specific regions of the mtDNA of Haematobia irritans, which have been associated with rearrangement events in other insect species: Amplicon I (including the tRNA^Trp, tRNA^Cys and tRNA^Tyr genes); Amplicon II (including the tRNA^Asp and tRNA^Lys genes) and Amplicon III (including the tRNA^Pro and tRNA^Thr genes). The amplicons I (1.362bp), II (1.727bp) and III (1.954bp) have the same gene content and gene order previously described in Drosophila yakuba. In order to improve the comparative analysis of these regions, these amplicons were also successfully amplified in Stomoxys calcitrans (stable fly) and Musca domestica (house fly), except for amplicon I of S. calcitrans, which amplification required additional optimization. No significative amplicon size variation was found based on these preliminary data. Structural characterization of arthropod mtDNA contributes for the understanding of the mitochondrial genome diversity and evolution. Financial  support: CNPq/PROFIX, FAPESP.