We report evidence for recombination in lichenized fungi based on sequenced nuclear DNA markers, judging from the incongruence of their gene genealogies. Recombining population structures were found in two phylogenetic species of Letharia, one species that is observed in nature to produce abundant sexual structures (ascomata) and another species that produces abundant clonal reproductive structures (soredia) and only rarely produces ascomata. To determine whether sexual reproduction was the cause of recombination in both species, we compared several variable loci in the ascomata and maternal tissue for evidence of outcrossing. All ascomata of both species were heterozygous for at least one locus, as would be expected to result from outcrossing and not from selling. Therefore, it appears that even in the sorediate species, rare sexual reproduction results in recombination. Copyright 2001 Academic Press.Index Descriptors: ascomycete; clonal reproduction; congruence of gene genealogies; heterozygosity; incongruence length difference/partition homogeneity test; Kishino-Hasegawa test; permutation tail probability test; phylogenetic species; sexual reproduction