Phytophthora root and crown rot is one the most important diseases of apple in Iran and worldwide. This research was performed first to recover oomycete species from infected apple roots and crowns, second, establish a reliable method for inoculation of apple rootstocks and third, evaluate disease resistance of some apple rootstocks in tissue culture media. Different infected samples were collected from the Horticultural Research Stations of Seed and Plant Improvement Institute in Karaj. Three Phytophthora cactorum isolates in addition to one Pythium sp. isolate were recovered out of 20 samples using semi selective media containing Carbendazim, Pimaricine and Rifampicin, 10 mg per liter each. Pathogenicity test was carried out on unripe pear fruits. For disease resistance evaluation experiments, five apple hybrid progenies (H1-H5) obtained through crossing between local genotype Morabbai mashhad and M9 plus the parents, M26, MM106 rootstocks and local genotype Azayesh were assessed to Phytophthora in tissue culture jars. Plant materials were micropropagated on QL media and inoculated with P. cactorum. The pathogen was amplified on the wheat grains so that the pathogen incited necrosis on the shoots inside the jars. The extent of necrosis was recorded after 18 days. Hybrid H5 was assessed as the most sensitive genotype to P. cactorum while hybrid H1 showed high level of resistance reaction.