The purple tomato variety ‘Indigo Rose’ (InR) is favored due to its bright appearance, abundant anthocyanins and outstanding antioxidant capacity.SlHY5is associated with anthocyanin biosynthesis in ‘Indigo Rose’ plants. However, residual anthocyanins still present inSlhy5seedlings and fruit peel indicated there was an anthocyanin induction pathway that is independent of HY5 in plants. The molecular mechanism of anthocyanins formation in ‘Indigo Rose’ andSlhy5mutants is unclear. In this study, we performed omics analysis to clarify the regulatory network underlying anthocyanin biosynthesis in seedling and fruit peel of ‘Indigo Rose’ andSlhy5mutant. Results showed that the total amount of anthocyanins in both seedling and fruit of InR was significantly higher than those in theSlhy5mutant, and most genes associated with anthocyanin biosynthesis exhibited higher expression levels in InR, suggesting thatSlHY5play pivotal roles in flavonoid biosynthesis both in tomato seedlings and fruit. Yeast two-hybrid (Y2H) results revealed thatSlBBX24physically interacts withSlAN2-likeandSlAN2, whileSlWRKY44could interact withSlAN11protein. Unexpectedly, bothSlPIF1andSlPIF3were found to interact withSlBBX24,SlAN1andSlJAF13by yeast two-hybrid assay. Suppression ofSlBBX24by virus-induced gene silencing (VIGS) retarded the purple coloration of the fruit peel, indicating an important role ofSlBBX24in the regulation of anthocyanin accumulation. These results deepen the understanding of purple color formation in tomato seedlings and fruits in anHY5-dependent or independent manner via excavating the genes involved in anthocyanin biosynthesis based on omics analysis.