The animal mitochondrial DNA (mtDNA) is a small, circular, simple and compact organized genome. Animal mtDNA gene content and general organization is well conserved (~37 genes), although rearrangements of tRNA genes (mainly) or coding-genes at “hotspot” regions have been reported in some organisms. The sequencing and molecular characterization of the mtDNA of the stable fly, Stomoxys calcitrans, are being conducted by two-steps LongPCR amplifications of the entire mitochondrial genome, shotgun library construction, assembling using phred/phrap/consed programs and comparative analysis on the Arthropodan Mitochondrial Genome Accessible database (AMiGA, http://amiga.cbmeg.unicamp.br). Preliminary results suggest an uncommon structural organization of the mtDNA of S. calcitrans at the putative control region (CR). A non-coding region of 96bp was described between the genes rRNA12S and tRNA^Ile, but no homologous motifs, based on conserved elements previously described for insect CR (including Muscidae), were identified in this intergenic region. LongPCR amplifications showed that the mtDNA of S. calcitrans is approximately 1Kb larger than the mitochondrial genomes of other Calyptratae species (Diptera). Based on these results, we are investigating the occurrence of gene duplications or rearrangements involving CR or other genetic element in the mtDNA of S. calcitrans. The complete sequencing of S. calcitrans mtDNA is being conducted to elucidate the mechanisms associated to the molecular evolution of gene organization in the mitochondrial genome of this parasitic species. The characterization of Arthropodan mitochondrial genomes is increasing the knowledge about the structural diversity and molecular evolution of this dynamic genomic system. Financial support: PROFIX/CNPq, CAPES, FAPESP.