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Abstract Background Fruit photosynthetic apparatus development comprises a series of biological processes which is essential in determining fruit development and quality formation. However, the understanding of the regulation of fruit photosynthetic apparatus development remains poor. Results In this study, we identified a transcriptional factor SlBES2, the closest homolog of BES1 and BZR1 in tomato BES1 family, is highly expressed in fruit at mature green (MG) stage and exhibited transcriptional inhibition activity. Down-regulation of SlBES2 resulted in fruits showing paler fruit than wild type at MG stage, in contrast, SlBES2-overexpressing tomato lines bore deeper green fruits. Notably, chlorophyll content and number of thylakoids per chloroplast in fruit was substantially increased in SlBES2-overexpressing lines, while markedly decreased in SlBES2-suppressing lines. Comparative transcriptome analysis revealed that multiple genes of the photosystem, chloroplast development and chlorophyll metabolism pathways were regulated by SlBES2. Further verification revealed that SlBES2 can significantly repress the transcriptional activity of SlNYC1 and Green-Flesh, and physically interact with protein SlHY5. Conclusions Collectively, this study demonstrated that SlBES2 plays an important role in regulating fruit photosynthetic apparatus development through either transcriptional repression of genes involved in chlorophyll breakdown, or posttranscriptional regulation of proteins associated with plant photomorphogenesis and chloroplast development. Our findings add a new actor to the complex mechanisms underlying photosynthetic apparatus during fruit development.