Abstract: Mitochondrial disorders are clinical phenotypes associated with abnormalities of oxidative phosphorylation (OXPHOS), the primary energy-producing process of all aerobic organisms. Disorders of OXPHOS are recognized as the most common inborn errors of metabolism affecting at least one in 5000 newborn children. Except for complex II, which is composed of proteins all encoded by nuclear genes, the other OXPHOS complexes are built up of both mitochondrial and nuclear DNA encoded proteins; so, assembling the OXPHOS complexes and fine tuning their activity require specialized regulatory mechanisms to optimize the cross-talk between the two genomes and ensure the coordinated expression of their relevant products. In this context, the characterization of nuclear genes encoding for mitochondrial proteins and of functional elements regulating their expression is of crucial importance to clarify real genetic causes of mitochondrial diseases, to assess the correct diagnosis and set up new and effective therapies. Despite the long evolutionary divergent time, many key pathways that control development and cellular physiology are conserved between Drosophila and humans, and about 70% of the genes associated with human diseases have direct counterpart in the Drosophila genome. To investigate on the functional constraints acting on the evolution and on the regulatory mechanism coordinating the expression of OXPHOS genes we have identified and characterized sequence and structure of these genes in three species of diptera, D. melanogaster, D. pseudoobscura and A. gambiae, and compared them with their human counterparts. Data obtained from this study have been annotated in the MitoDrome2 database. The availability of data produced by our study in MitoDrome2 is expected to be particularly useful for biologists and clinicians interested in studies of functional genomics related to mitochondrial biogenesis, metabolism and to their pathological dysfunctions.