To compare genetic variation among four geographically distant populations of the fungus species Melampsora epitea causing willow rust, a two-primer combination was used for ALFP fingerprinting of 24 isolates from Sweden, along with 10 from France, 24 from Northern Ireland, and 35 from Chile. The banding patterns of all 93 isolates were easily distinguished and revealed polymorphism among individuals within and between the four M. epitea populations. No clustering on the dendrogram could be attributed to country of origin, or almost equivalently, country of origin correlated poorly with genetic distance, suggesting that the geographically distant populations developed collectively as a metapopulation, instead of separately.