During a study on population genetics of three species of Cladonia using the nuclear ribosomal 18S DNA, two species contained group I intron-like sequences located in positions 788 and 940 with reference to the E. coli 16S rDNA gene. The intron in position 940 was not typical of group I introns and had previously been described only from the Parmeliaceae and Lecanoraceae, but here we report the occurrence of this intron in the Cladoniaceae. The intron in position 788 had characteristics of group I introns and had previously been reported from the Physciaceae. In this paper we provide for the first time a putative RNA fold for the nS788 intron, compare the secondary RNA structure of the Cladonia group I introns (nS788 and nS940) to that of other taxa, and infer a phylogenetic history among 15 members of the Lecanorales based on the evolutionary history of the nS788 group I intron. The RNA fold for nS788 contained two optional hairpins, P2.1 and a potentially newly described hairpin referred to as P5.1. The phylogenetic hypothesis supports the monophyly of the genus Cladonia. It also supports the separation of two large groups in the Physciaceae; the Buellia-group and the Physcia-group.