The mammalian target of rapamycin (mTOR) pathway is important for nutrient signalling and the regulation of life span. Rapamycin, therefore, has attracted attention as a pharmacological means to mimic the beneficial effects of dietary restriction that extends longevity. Mitochondria also have important roles in nutrient signalling and aging, but the mechanisms by which mTOR alters mitochondrial activity are not fully understood and the contribution of the mitochondrial genotype to this effect is unknown. In this work (p. 2282), Eugenia Villa-Cuesta, Marissa Holmbeck and David Rand use Drosophila mitochondrial genome replacement strains obtained from crossing D. melanogaster and D. simulans to test whether genes encoded in mitochondrial DNA (mtDNA) affect the mTOR pathway. They find that treatment with rapamycin increases the rate of mitochondrial respiration and the activity of complex II of the electron transport chain, and decreases the production of mitochondrial H2O2. Furthermore, by using metabolomics analysis of the different mitochondrial genotypes, the authors show that distinct shifts in the profiles of carbohydrates and amino acids of isolated mitochondria as compared with those of the whole organism. Interestingly, these effects are abrogated when divergent mitochondrial genomes from D. simulans are placed into a common nuclear background. This disrupts the crosstalk between nuclear and mitochondrial genomes, suggesting that the effects of rapamycin on mitochondrial metabolism depend on mtDNA genes. Taken together, this study, for the first time provides evidence that genes encoded in mtDNA are mediators of the mitochondrial metabolic effect of rapamycin. The findings also highlight the need for further studies in order to fully understand the potential benefits of this compound.