Common root rot, due to Aphanomyces euteiches, is a very damaging disease of legumes, especially pea, in many countries. Several consistent quantitative trait loci controlling partial resistance were identified in different pea genetic pools. Genomic basis of resistance to A. euteiches was investigated in the model legume Medicago truncatula in order to identify candidate genes underlying Aphanomyces resistance loci and analyze synteny of resistance loci between pea and M. truncatula. High density genome-wide association mapping was conducted in a collection of 179 M. truncatula accessions, for resistance to five reference A. euteiches isolates of main pea and alfalfa pathotypes. Two main genomic regions carrying candidate SNPs were associated with resistance. The first one corresponded to an F-box protein encoding gene at the prAe1/AER1 loci on chromosome 3 and the second one to a NBS-LRR resistance protein encoding gene underlying a new resistance locus on chromosome 4. The candidate genomic regions identified in M. truncatula were projected to a pea consensus genetic map carrying 1250 SNP markers anchored to M. truncatula genome. The F-box gene syntenic region co-located with the minor QTL Ae-Ps3.2 on pea LGIII and the NBS-LRR gene syntenic region was positioned about 50 cM far from the major QTL Ae-Ps7.6 on pea LGVII. Work is in progress to precise synteny between Aphanomyces resistance loci in pea and M. truncatula and to search for pea genes orthologous to the M. truncatula candidate genes identified