A total of 567 isolates of the rust fungus Melampsora lini were collected from nine populations of the Australian endemic host, Linum marginale, growing over a distance of 100 km within the Kosciusko National Park, New South Wales, Australia, Collections at each site were made over 2–4 consecutive years and races were identified using a set of 12 lines of L. marginale carrying different resistances. Four races dominated the combined metapopulation: three were widespread and common, while the fourth (with the largest range of virulence of the four) was widespread but, with the exception of one population, rarely occurred at a frequency of greater than 15%. This general pattern was maintained over all years. Individual populations were generally composed of one or two dominant races plus a variable number of others represented by only a few isolates. The diversity of populations (Shannon-Weaver index) showed little variation either within populations across years or between populations within years. At the individual population level, significant year-to-year variation was detected in the racial structure of four populations. However, when compared in terms of virulence on individual members of the differential set, significant year-to-year variation occurred in only two of these populations. Analysis of the data suggested that the pathogen exists as an overall metapopulation (a set of local populations) with high levels of migration occurring between individual populations.