This study reports on the complete mitochondrial genomes of ten species of lichenized fungi within the order Arthoniales, including the genera Arthonia, Chrysothrix, and Opegrapha: A. kermesina, A. quintaria, A. cupressina, A. rubella, A. ruana, C. susquehannensis, C. onokoensis, O. vulgata, O. moroziana, and O. corticola. Phylogenetic analysis of these species shows the order Arthoniales forming a distinct clade, and provides evidence that the order is more distantly related to other previously annotated species. Protein synteny varied greatly across all species, with no conserved order across species. However, linkage between certain genes was observed across all annotated species. Species within the genus Arthonia showed significant differences from previously sequenced lichenized species, including a distinct lack of retro-transposable elements, trans-splicing of nad4, and a lack of intronic regions within protein coding genes. In addition, atp9 was not present in O. corticola or C. susquehannensis, while still present within other species of their genera. Previous research found atp9 to either be present or completely absent in every annotated species within a genus. This finding may change our understanding of genetic changes in obligate symbiotes, and further research may reveal new patterns of how these changes occur.