Genetic variation of the fungal plant pathogenSclerotinia sclerotiorum(Lib.) de Bary was examined using DNA fingerprinting. Seventy‐five isolates ofS. sclerotiorumwere collected from four populations in the South Island of New Zealand. DNA fingerprints were generated for each isolate by Southern blotting using a cloned repetitive sequence, pLK44.20, as a probe. The 47 different fingerprints produced revealed a high level of variation both within and between populations. Comparison of fingerprint similarities indicated substantial local movement of isolates but gave little evidence for long‐range dispersal. A subset of the isolates was tested for mycelial compatibility. Pairs with identical or highly similar DNA fingerprints gave compatible reactions, whereas isolates whose fingerprints were dissimilar were incompatible. The high level of variation observed in New Zealand populations ofS. sclerotiorumhas relevance for control of diseases caused by this pathogen, as any method of disease control must be effective across the range of pathogen variation.