To investigate the association between, and the reproductive modes of, mycobiont and photobiont in the lichen Parmotrema tinctorum, microsatellite markers (SSR markers) were developed for both bionts and genotypic analysis was performed for thalli in a Pinus thunbergii forest. In a within-thallus analysis, tissue pieces were sampled from many portions within each of five thalli. Within-thallus variation for both mycobiont and photobiont differed among the thalli investigated, suggesting that a single thallus can be derived from either a single mycobiont origin with or without occasional changes in the photobiont, or fusion of several independent thalli. In the within-tree analysis, thalli with the same genotypes were found on individual trees, suggesting the presence of short-distance isidium dispersal. In the within-stand analysis, genotypically similar photobionts tended to be associated with the same mycobiont genotype, suggesting the participation of local dispersal via isidia. The overall index of association (IA) for the mycobiont in the stand probably indicates the dominance of sexual reproduction, in contrast to that of the photobiont, where dominance of asexual reproduction is suggested. IA's of mycobiont and photobiont were also calculated for thalli collected from larger areas, where there is a signature for sexual reproduction for photobiont.