Here we incorporate molecular sequence data (ITS, IGS, mtLSU, RPB2) to test the hypothesis of strict clonality in the lichen-forming fungus Thamnolia vermicularis. Recombination was rejected by most methods, though, a small number did detect recombination. We intepret these analyses as mostly supporting the hypothesis of strict clonality. We were unable to determine if the recombination detected was the result of rare recombination events in recent time, historic recombination, or false positives by certain methods. In addition, we investigated whether chemotypes in T. vermicularis formed monophyletic groups. Molecular sequence data suggest that the two chemotypes do not form well-supported, monophyletic lineages. Chemotypes were found with identical haplotypes and some populations were composed of more than one haplotype. Our data suggest that there is not a simple dichotomy between chemotypes in T. vermicularis, which may be due to rare or historic recombination, repeated chemotype evolution or incomplete lineage sorting.