Genetic variation within and among vegetative compatibility groups (VCGs) of Stereum sanguinolentum isolates was investigated with various geographical distances. DNA fingerprints were made using the M13 core sequence as a primer. A total of 113 isolates from 12 plots in Sweden, Finland and Lithuania were studied. Each VCG produced a discrete group of banding patterns. Among 20 isolates from the largest VCG, G1, the incidence of identical banding patterns was 24% within a sample plot, 8% among sample plots within a country, and 0% among countries. In the other 15 VCGs that comprised two and more isolates, corresponding percentages were 42%, 30% and 0%. Average band-sharing indices (ABSIs) within VCGs decreased with increasing geographical distance: for isolates from VCG G1, ABSI was 91.3% within sample plots, 85.4% among sample plots within a country, and 79.2% among countries. Corresponding figures for the other 15 VCGs were 97.0%, 92.7% and 80.4%, respectively. Among VCGs similarities were significantly lower (P < 0.001) and the trend of decreasing similarity with larger geographical distances was less pronounced: ABSI within sample plots was 73.7%, among sample plots within countries 73.8%, and among countries 71.1%. However, the similarity of populations as compared within and between countries differed significantly (P < 0.001), suggesting geographical differentiation between S. sanguinolentum populations separated by 400 km and the Baltic sea. Calculations of GST clearly indicated geographical population subdivision within the large VCG but not among the total sample. In summary, the results show population structure of inbred lines within VCGs containing closely related strains in local populations and more distant relationships among populations.