Genetic diversity in symbionts of the lichen Cladonia arbuscula was investigated. Forty-eight specimens of Cladonia arbuscula located within a 2 km range at Payuk Lake in Manitoba were collected. Population structure and method of symbiont transmission in C. arbuscula were inferred by examining the presence or absence of introns in the nuclear small subunit (SSU) ribosomal DNA (rDNA) of the mycobiont and restriction fragment length polymorphism (RFLP) of the internal transcribed spacer (ITS) rDNA in the photobiont. The mycobiont showed a high level of genetic variation and the photobiont a low level of variation within the small geographic range studied. An analysis of molecular variance of fungal genotypes showed significant population subdivision for the mycobiont when the data were analysed at P=0·05. No population subdivision was detected when P=0·001. The photobiont also showed no population subdivision. Photobiont genotypes did not correlate with mycobiont genotypes suggesting the symbionts were not transmitted together in the same propagule. Multiple fungal genotypes were also detected in C. arbuscula and possible explanations were discussed.