Boreal forest coarse woody debris (CWD) is a dynamic substratum for bryophytes and lichens. However, few studies have examined species and genetic diversity associated with different degrees of CWD decay. The objectives were to examine species richness and diversity, to compare geographic locations and decay classes, and to conduct an indicator species analysis. Fifty lichen and 22 bryophyte species were found, with changes in species richness and diversity associated with progressive wood decay. Indicator species (Cladonia arbuscula, C. gracilis, Parmeliopsis hyperopta, Pleurozium schreberi, and Pylaisiella polyantha) were associated with particular decay classes. Genetic diversity and gene flow in the most common lichen Cladonia arbuscula were explored by Randomly Amplified Polymorphic DNA (RAPDs) showing genetic structure between populations on different substrata. The identification of indicator species and species diversity has implications for forest management and conservation efforts to ensure the genetic and species diversity is maintained.