A synteny based positional cloning approach was started to clone the pea SYM2 gene by using locally conserved genome structure with the model plant Medicago truncatula. We reported that a pea marker tightly linked to SYM2 was used to screen a M. truncatula BAC library, and two contigs named C1/C2 and C3 were constructed that are both located on the long arm of M. truncatula chromosome 5 and separated by 9 cM. C1/C2 is highly microsyntenic to the pea SYM2 genomic region and corresponds to the M. truncatula SYM2-orthologous region, which is delimitated to 350 kbp. In this manuscript we analyze the distribution in the three contigs of 22 sequences and their homologues, including eight C1/C2 and two pea RFLP markers linked to SYM2. Among the analyzed sequences are several different (receptor) kinase-like gene sequences and two classes of LRR-containing resistance protein-like sequences. From all the studied sequences only four detected homologous sequences in C3, and their distribution is comparable in C1/C2 and C3, suggesting that a 70-kbp and a 120-kbp segments of these two contigs, respectively, arose through a duplication. The implications of these findings for the cloning of SYM2 are discussed.