Morphological characters can vary to an extent that makes it difficult to separate the two morphologically and chemically similar species Xanthoria aureola and X. parietina for an inexperienced field biologist. They occur frequently in mixed stands on seashore rocks on the western coast of Norway. We examined (1) whether a simple method like RAPD-PCR could confirm the distinction between the two species previously reported on the basis of DNA sequences, and (2) whether infraspecific DNA and RAPD data from X. parietina were congruent. We also checked whether the RAPD band scoring procedure could affect the results. Results show that (1) RAPD distance matrices based on band scorings performed independently by the two authors were always congruent and differences never affected conclusions, (2) RAPD clearly distinguishes between X. parietina and X. aureola in a way that is fully congruent with a classification based on DNA sequence data, and (3) there was no significant congruence between infraspecific distances based on DNA sequences and RAPD data in X. parietina. The latter observation may be taken as support for a previously published report of low levels of recombination in X. parietina, which stands in contrast to statements of obligate homothallism in that species.