Two inoculation techniques were applied to investigate the effects of season and isolate variability on apple rootstocks in response to Phytophthora cactorum infection. Shoots of rootstocks MM106 and MM109 were inoculated in vitro with a single P. cactorum isolate once a month for 26 months. Rootstock susceptibility measured as lesion lengths generally cycled to a low level during dormancy in winter and to a high level during active growth in summer. Direct inoculation on excised stems was used to assess the relative aggressiveness of P. cactorum isolates. Bark was removed and stems were inoculated with mycelial discs of various P. cactorum isolates. Rootstock × isolate interactions complicated this evaluation, causing variable results. However, differences in relative aggressiveness of isolates were apparent during the dormant stage of apple stems. It was shown that the season during which evaluation was performed and variation of isolate aggressiveness affected the host reaction to P. cactorum infection.