Lichen assemblages and their secondary metabolites may be influenced by the broader habitat. More specifically, the function of the thallus structure within a species may influence the production of some secondary metabolites. The objectives of this study were to examine thallus variation in secondary metabolites for one genus, Stereocaulon, and to compare the diversity of lichen assemblages and their secondary metabolite distributions in the boreal forest of northwestern Manitoba. Five sites in each of three study regions were selected (Sherridon, North Star, and Athapap), around the presence of a Stereocaulon thallus. All ground lichen species were collected from five quadrats within each site totaling 75 quadrats. Lichen species were identified and thin-layer chromatography was performed to identify secondary metabolites. A total of 59 ground lichen species and 20 secondary metabolites were identified. This study showed that norstictic acid and constictic acid were absent from the pseudopodetia but present in the apothecia and phyllocladia of Stereocaulon tomentosum only. It also showed that species richness was different between one region (Athapap) and the other two regions (North Star and Sherridon). North Star and Sherridon had the highest species richness and number of metabolites and Athapap had the lowest.