This study examined the beneficial effects of black rice anthocyanin extract (BRAE), which provides as an excellent source of dietary antioxidants, on the lifespan of fruit flies and the underlying molecular mechanisms. Results showed that supplementation of BRAE extended the lifespan of fruit flies by 20% and retarded the loss of locomotor function. Comparison of mRNA transcriptome profile between fruit flies of 20 days and 50 days after the start of normal diet and normal diet supplemented with BRAE (5 mg/mL) identified 6687 differentially expressed coding genes. A large number of these differentially expressed mRNAs were enriched in KEGG (Kyoto Encyclopedia of genes and genomes) analysis. KEGG pathway analysis demonstrated that up regulation in the glutathione metabolism, neuroactive ligand-receptor interaction, and down regulation in FoxO signaling pathway, mTOR signaling pathway were most likely affected by supplementation of BRAE. In addition, several genes, including Zw (Zwischenferment), GstD2, GstE1, Gpx, Gclm, Tsc1, 4E-BP, DopR and D2R, which were involved in the pathways mentioned above, could be regulated by the supplementation of BRAE. Together, the results implicated that the expression of most of the mRNAs in fruit fly were closely associated with BRAE diet, which could provide a resource of mRNAs related in the field of aging and aging-related disease.