Tomato and peach are two important model species belonging to the families Solanaceae and Rosaceae, respectively. Recently, more and more sequence data generated from their whole genome sequencing projects can be used for bioinformatic analysis. Microsynteny analysis for tomato and peach were conducted to detect conserved syntenic blocks using high quality genetic and physical maps. A large number of microsyntenic regions were detected through three com-parisons: comparison between tomato genetic map and peach physical map, between tomato physical map and peach ge-netic map, and between tomato physical map and peach physical map. Most of the syntenic blocks were short, and each block contained a small number of conserved gene pairs (261 syntenic blocks with only two homolog pairs, and 36 syntenic blocks with more than two homolog pairs). Tomato and peach had noncontinuous fragmentary microsynteny and some syntenic groups composed of complex networks among different chromosomes or BAC contigs. After comparing the ho-mologous proteins with tomato fruit-related EST libraries, a total of 9 proteins were found in different syntenic groups re-lating to fruit development and ripening. Microsynteny identified in this study could facilitate further investigation of fruit development and ripening in these two distantly related species.