Dietary restriction (DR) is the most consistent means of extending longevity in a wide range of organisms. A growing body of literature indicates that mitochondria play an important role in longevity extension by DR, but the impact of mitochondrial genotypes on the DR process have received little attention. Mitochondrial function requires proper integration of gene products from their own genomes (mtDNA) and the nuclear genome as well as the metabolic state of the cell, which is heavily influenced by diet. These three-way mitochondrial-nuclear-dietary interactions influence cellular and organismal functions that affect fitness, aging, and disease in nature. To examine these interactions in the context of longevity, we generated 18 "mito-nuclear" genotypes by placing mtDNA from strains of Drosophila melanogaster and D. simulans onto controlled nuclear backgrounds of D. melanogaster (Oregon-R, w1118, SIR2 overexpression and control) and quantified the lifespan of each mitonuclear genotype on five different sugar:yeast diets spanning a range of caloric and dietary restriction (CR and DR). Using mixed effect models to quantify main and interaction effects, we uncovered strong mitochondrial-diet, mitochondrial-nuclear, and nuclear-diet interaction effects, in addition to three-way interactions. Survival analyses demonstrate that interaction effects can be more important than individual genetic or dietary effects on longevity. Overexpression of SIR2 reduces lifespan variation among different mitochondrial genotypes and further dampens the response of lifespan to CR but not to DR, suggesting that response to these two diets involve different underlying mechanisms. Overall the results reveal that mitochondrial-nuclear genetic interactions play important roles in modulating Drosophila lifespan and these epistatic interactions are further modified by diet. More generally, these findings illustrate that gene-by-gene and gene-by-environment interactions are not simply modifiers of key factors affecting longevity, but these interactions themselves are the very factors that underlie important variation in this trait.