The crop legume pea (Pisum sativum) is genetically well characterized. However, due to its large genome it is not amenable to efficient positional cloning strategies. The purpose of this study was to determine if the model legume Medicago truncatula, which is a close relative of pea, could be used as a reference genome to facilitate the cloning of genes identified based on phenotypic and genetic criteria in pea. To this end, we studied the level of microsynteny between the SYM2 region of pea and the orthologous region in M. truncatula. Initially, a marker tightly linked to SYM2 was isolated by performing differential RNA display on near-isogenic pea lines. This marker served as the starting point for construction of a BAC physical map in M. truncatula. A fine-structure genetic map, based on eight markers from the M. truncatula physical map, indicates that the two genomes in this region share a conserved gene content. Importantly, this fine structure genetic map clearly delimits the SYM2-containing region in pea and the SYM2-orthologous region in M. truncatula, and should provide the basis for cloning SYM2. The utility of the physical and genetic tools in M. truncatula to dissect the SYM2 region of pea should have important implications for other gene cloning experiments in pea, in particular where the two genomes are highly syntenic within the region of interest.