Usnea aurantiaco-atra is the dominant flora around King George Island, Antarctica, whose specimens exhibited various phenotypes, even for those with the same ITS sequences in both mycobiont and photobiont. A comprehensive analysis of morphological traits of U. aurantiaco-atra including the reproductive structures, growth forms and ornamentation, cross section of the branches, and the substratum was carried out. Four arbitrary groups were identified based on their reproductive characters, but these groups cannot be distinguished from molecular phylogenetic trees based on fungal or algal ITS sequences. Further, the complicated morphological diversity of the thalli with the same ITS haplotypes in both mycobiont and photobiont suggest that some other factors in addition to the symbionts could influence the morphology of lichens. This implies that lichen is indeed a complex-mini-ecosystem rather than a dual symbiotic association of fungus and alga. Also, a lichenous fungi Phacopsis sp. was identified based on its anatomical characters and ITS sequence, which was also responsible for the black burls-like structures on U. aurantiaco-atra.