Rosaceae is a plant family with over 3,000 species including a number of economically important fruit-bearing species. Although plants in Rosaceae family have similar basic flower structure, their fruit flesh comes from distinct floral tissues. In drupe fruit, such as peach and plum, the ovary wall becomes enlarged and fleshy. In pome fruit, such as apple and pear, the fruit fleshy is mainly derived from the hypanthium that encases the ovary. In drupetum fruit, such as raspberry, numerous unfused ovaries each grow into a fleshy drupelet. In achenetum fruit, such as strawberry, the numerous unfused ovaries eventually dry up, but the receptacle, the stem tip that supports these ovaries, instead develops into the fruit flesh. By investigating and comparing the transcriptomes from these four Rosaceae fruits, peach (Prunus persica), apple (Malus x domestica), strawberry (Fragaria vesca), and raspberry (Rubus idaeus), at the earliest stages of fruit development, we gain important insights into the genetic mechanisms underlying fleshy fruit diversity. The expression of B class MADS-box genes, PISTILLATA, APETALA3 and TM6, shows negative correlation with the ability to form fleshy fruit tissues. Based on RNA transcript and phylogenetic analysis, FBP9, a MADS-box gene related to the E class, appears to be necessary but insufficient for flesh formation. In addition to the regulatory roles MADS-box genes play in fruit identity specification, extensive lignification of the strawberry ovary wall may contribute to the inability of strawberry ovary to become fleshy. Finally, a database (ROsaceae Fruit Transcriptome database, ROFT) is established for researchers to query for orthologous genes and their expression patterns during fruit development in the four species as well as to query for the tissue-specific and tissue- and stage-specific genes. Together, these findings provide the framework for functional investigations of fruit type specification and insights into the evolution of diverse fruit types in the Rosaceae family. The knowledge gained will advance our understanding in the evolution of fleshy fruits, a defining feature of angiosperm, and enable the creation of new fruit types for consumers.