Phaeomoniella chlamydospora is considered to be the causal agent of Petri disease. This disease causes decline of grapevines in most grape growing regions of the world. Genetic variation within 39 New Zealand isolates of Phaeomoniella chlamydospora was compared to six isolates from Italy using randomly amplified polymorphic DNA (RAPD), randomly amplified microsatellites (RAM), amplified fragment length polymorphism (AFLP), and universally primed polymerase chain reaction (UP-PCR). Using each method, genetic variation within New Zealand and Italian isolates of P. chlamydospora was shown to be low, with a maximum of seven genetic groups identified by each primer. The greatest amount of genetic variation was shown using AFLP analysis, with 21 different groups identified. RAPD, AFLP and UP-PCR primers detected inter-vineyard, intra-vineyard and intra-vine variation of New Zealand isolates. A subset of five New Zealand and one Italian isolate was further investigated using mycelial compatibility groups (MCGs). One MCG was identified, supporting low genetic variation within P. chlamydospora isolates. Low genetic variation within the New Zealand and the Italian populations suggests that asexual reproduction predominates, and the presence of intra-vineyard and intra-vine variation in New Zealand indicates that multiple introductions have occurred.