Little is known about species diversity and genetic structure of populations of lichens and bryophytes in the Sandilands Provincial Forest in Manitoba. This study investigated the current species diversity of lichens and bryophytes in the area. It also examined the population structure and gene flow in the lichen (Cladonia arbuscula) with the highest cover and second most frequent occurrence, and bryophyte (Pleurozium schreberi) with the highest frequency and percent ground cover. Analysis of Molecular Variance (AMOVA) of the presence and absence of group I introns in the fungal small subunit (SSU) nuclear ribosomal DNA (rDNA) and Restriction Fragment Length Polymorphisms (RFLP) of the algal Internal Transcribed Spacer (ITS) rDNA suggests that low levels of gene flow were occurring in the fungus while a single algal genotype was maintaining the lichen association. Similarly, Interspersed Simple Sequence Repeat (ISSR) markers of the bryophyte suggested low levels of gene flow. The examination of variation in both lichen symbionts and a bryophyte, dominant within the same habitat, is a novel aspect of this study. Both these widespread species, dominating the understory in mature jack pine forests, exhibited low levels of sexual reproduction.