Three aspects of Xanthoparmelia cumberlandia and Xanthoparmelia coloradoënsis populations found at two elevations are explored: clustering of secondary chemicals and the resulting implications for taxonomic distinctions, the usefulness of thallus size as an indirect measure of sexual fecundity, and the frequency of sexual reproduction. First, we use clustering of 46 chemicals produced by X. cumberlandia and X. coloradoënsis to evaluate the adequacy of the current taxonomic distinction between them. Using principal components analysis and UPGMA, we find that the currently recognized species boundaries indicated by the presence of stictic acid in X. cumberlandia and salazinic acid in X. coloradoënsis are supported by distinct differences in their chemotypes (combinations of secondary chemicals). Norstictic acid, which the literature also associates with X. cumberlandia, is found frequently in both X. cumberlandia and X. coloradoënsis, and is not a good distinguishing characteristic. No chemical difference between sexually fecund and sterile individuals was found. Second, we test the claim that thallus size can be used as an indirect measure of sexual fecundity. By comparing the number of apothecia, the total area of the apothecia, and the presence or absence of apothecia with thallus area, we found positive correlations between these measures of sexual fecundity and thallus size which are statistically significant. However, the total variation explained by these predictors is limited, and is significantly affected by elevation and micro-environmental features such as proximity to trees. We conclude that size is not a reliable synonym for sexual fecundity in X. cumberlandia and X. coloradoënsis. Third, we make inferences concerning the frequency of sexual reproduction based on the frequency of sexual structures, rare chemicals, and unique chemotypes. We predicted that sexual reproduction would be more frequent at lower elevations, consistent with a common pattern found in plants and animals. The frequency of sexual structures indicates that sexual reproduction is more common at the lower elevation, while frequency of rare chemicals and chemotypes implies that outcrossing is more common at the upper elevation. Since these indicators lead to opposing conclusions, we encourage the use of molecular markers to estimate the frequency of outcrossing directly.