Genetic variation of the haploid canker pathogen fungus Gremmeniella abietina was investigated by RAPD marker analysis. A total of 126 single pycnidia isolates of G. abietina were sampled from one Pinus contorta plantation in northern Sweden. Average Nei's gene diversity over 32 putative RAPD loci was 0·29. Multilocus genotype analysis revealed 85 different genotypes among the 126 isolates sampled, of which 66 genotypes were detected only once. Nineteen genotypes were detected more than once among 41 isolates, representing 32·5% of clonal fraction of the sampled population. Gametic disequilibrium tests of the sampled population revealed significant associations between 29·6% (147 of 496) of the RAPD loci. When the clonal fraction was removed from the data set, the number of significant pairwise loci combinations decreased from 147 to 73 (14·7%), indicating a high degree of random mating. These results are consistent with previous field observations suggesting that sexual fruiting bodies of G. abietina were common in northern Scandinavia. The high genetic variability detected in the population also suggests that the population was founded by a relatively large number of unrelated genotypes.