Phytophthora root rot, caused by Phytophthora medicaginis, is a major disease of alfalfa (Medicago sativa) in North America and Australia. At least six different loci, with several modes of inheritance, conferring resistance to P. medicaginis have been identified through inheritance studies across a number of M. sativa genetic backgrounds. Here we report for the first time the genomic location of QTL for resistance to P. medicaginis in a tetraploid alfalfa genotype WA272 from the Australian cultivar Aquarius. A genetic linkage map was constructed using SSR (simple sequence repeat, or microsatellite) markers of known genomic location from existing M. sativa linkage maps and Medicago truncatula linkage and physical maps. Phenotypic information was obtained from the mapping population using cotyledon and root infection courts, and disease reaction and disease severity were assessed. Large effect QTL for root reaction were identified on linkage groups 2 and 6, explaining 32% and 22% of the phenotypic variation respectively. Additional QTL associated with root resistance were located on linkage groups 5 and 7 and explained 10% and 14% of the phenotypic variation respectively. QTL for root disease severity and cotyledon reaction co-located on each of linkage groups 2, 5, 6 and 7. Markers will be evaluated to aid marker assisted selection.