Pseudevernia furfuracea is a shrubby lichen commonly found around the Baltic Sea. The lichen appears to reproduce mainly by producing isidia, propagules of the lichen cortex. It is very morphologically and chemically diverse and can be found on different substrates, such as nutrient poor bark trees and rocks. The main objective of this study was to describe genetic variation in the ITS region and link this to variations in morphology, substrate ecology and secondary chemistry. In total, 36 specimens of P. furfuracea were collected from 21 sites in Sweden, Finland and Estonia. Seven haplotypes were distinguished in the ITS region. A statistically significant connection between haplotype and colouration of the lichen was found. Lighter coloured specimens of P. furfuracea are more likely to be of the ancestral haplotype. No other significant correlations between the different characteristics studied were found, suggesting that P. furfuracea should be regarded as a single species within the Baltic Sea area. This is also supported by the haplotype network.