The performance of 14 apple rootstock genotypes was tested in orchard soil mixes from three NY apple growing regions by comparing the growth in untreated soils to that in pasteurized soils. Several rootstocks had a higher mortality in the pasteurized soil treatment than in the untreated soil. Phytophthora cactorum was isolated from the roots of the dead apple rootstocks. These results prompted us to study the role of the stoolbed microbial community as possible source for members of the microbial rhizosphere and root pathogen communities in transplanted apple seedlings. The rhizosphere community composition of bacteria, fungi and oomycetes of the stoolbeds was compared to that in the pasteurized and non-pasteurized soil using a DNA fingerprinting method (PCR-DGGE). For both fungi and bacteria, the rhizosphere community composition of the stoolbeds was more similar to that in the non-pasteurized soil than that in the pasteurized treatment. However, for the oomycetes, a DNA fingerprint band in the same position as the P. cactorum control was detected in stoolbed samples as well as in pasteurized and non-pasteurized soils. The identification of species represented by this band is currently under way.