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. A number of theories support the advantages of genetic recombination, with Muller's Ratchet (Muller 1964), Kondrashov's Hatchet (Kondrashov 1993) and the Red Queen (Bell 1982) appearing among the leaders (Normark et al. 2003). Muller's Ratchet and Kondrashov's Hatchet both argue that deleterious mutations are purged through recombination, while the Red Queen argues that recombination allows organisms to generate new genetic combinations that enable them to escape parasitism (Bremermann 1980; Hamilton 1980; Jaenike 1978; Lloyd 1980). Despite the advantages genetic recombination confers, a number of ancient asexual lineages exist (summarized in Normark et al. 2003). While some of these lineages may truly lack recombination, molecular data have revealed that some putative asexuals exhibit evidence of genetic recombination (Burt et al. 1996; Gandolfi et al. 2003; Geiser et al.