Abstract: Microbial communities were analysed from bulk soil and rhizosphere samplescollected from a rotational field trial investigating the effect of shortened rotations on yield ofoilseed rape (OSR). Total DNA was extracted from the samples and Terminal RestrictionFragment Length Polymorphism (TRFLP) analysis was carried out to obtain community profilesfor fungi and bacteria from selected rotational treatments. Cloning and sequencing were alsocarried out to identify microorganisms that had dominant peaks in the TRFLP profiles. Changesin the microbial communities were seen with the different rotations, and in particular the obligateparasite Olpidium brassicae was found to be significantly more abundant in rhizosphere samplesfrom continuously cropped OSR than those from virgin OSR. Other fungi showing significantdifferences in abundance with various rotations included Pyrenochaeta sp. and Verticilliumnigrescens. However, the involvement of these microorganisms in yield decline of OSR grown inshort rotation has not yet been elucidated.