Armillaria root rot (ARR) caused by Armillaria solidipes, A. tabescens, and A. mellea is one of the principal causes of premature mortality of Prunus species (stone fruit trees) in the United States. Presence of a high level of Armillaria spp. not only kills trees, but also passes a “death sentence” on Prunus spp. orchards. Unfortunately, there is no known control of ARR. The easiest strategy for growers to mitigate tree losses from Armillaria spp. would be to utilize Armillaria resistant rootstock. Our objective was to determine variation in tolerance of 24 different Prunus germplasms to Armillaria spp. by utilizing wounded and intact root/shoot periderm inoculation assays and anti-fungal screening assays. The success of fungal penetration through wounded and intact root/shoot periderm and the length of fungal colonization were significantly different among various Prunus germplasms. Armillaria spp. successfully invaded peach germplasms and were unable to penetrate through the intact bark of most of plum and plum derived roots and cherries, P. avium, and P. maackii. Histological examination of the inoculated roots revealed that the tolerant germplasms had the ability to form barrier zones to deter the invading fungus. Also, the concentration of anti-fungal compounds was relatively higher in germplasms that that were less prone to Armillaria spp. infection. Our results imply that intra-species variation in tolerance of Prunus spp. to Armillaria spp. exists.