Fleshy fruits are important worldwide crops that are rich sources of useful and functional compounds in the human diet. Although fruit ripening has been extensively studied, early fruit development has not been paid much attention despite its contribution to the sensorial and nutritional quality of the fruit. This study aimed at identifying candidate genes involved in early fleshy fruit development that can contribute to the control of final fruit size and composition by comparative analysis of tomato and grape genes. By mining public sequences and microarray database, we identified 23 transcription factors belonging to 14 classes (AP2-EREBP, ARF, bHLH, bZIP, C2C2-GATA, FHA, GeBP, GRAS, HB, LIM, MYB, PBF-2-like, SBP and WRKY) as candidate regulatory genes for early fruit development. The function of these candidate genes will be confirmed by several reverse genetic approaches using the miniature tomato cv. Micro-Tom.