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Premise of the study: The locally rare, haploid, lichen-forming fungi <i>Bryoria capillaris</i>, <i>B. fuscescens</i>, and <i>B. implexa</i> are associated with boreal forests and belong to <i>Bryoria</i> sect. <i>Implexae</i>. Recent phylogenetic studies consider them to be conspecific. Microsatellite loci were developed to study population structure in <i>Bryoria</i> sect. <i>Implexae</i> and its response to ecosystem disturbances. Methods and Results: We developed 18 polymorphic microsatellite markers using 454 pyrosequencing data assessed in 82 individuals. The number of alleles per locus ranged from two to 13 with an average of 4.6. Nei's unbiased gene diversity, averaged over loci, ranged from 0.38 to 0.52. The markers amplified with all three species, except for markers Bi05, Bi15, and Bi18. Conclusions: The new markers will allow the study of population subdivision, levels of gene introgression, and levels of clonal spread of <i>Bryoria</i> sect. <i>Implexae</i>. They will also facilitate an understanding of the effects of forest disturbance on genetic diversity of these lichen species.