In this study, the complete mitochondrial genome ofCladonia subulata(L.) FH Wigg was sequenced and assembled and then compared with those of otherCladoniaspecies. The mitogenome ofCladonia subulata, the type species ofCladonia, consisted of a circular DNA molecule of 58,895 bp 44 genes (15 protein-coding genes, 2 rRNA genes, and 27 tRNA genes). The base composition had shown an obvious AT preference, and all 27 tRNA genes formed a typical clover structure. Comparison with other 7Cladoniaspecies indicated that the duplication/loss of tRNAs had occurred during evolution, and introns appeared to explain the variation incox1 genes inCladonia, the mitochondrial genome tends to be generally conservative and local dynamic changes. Repeat sequences were mainly located in gene intervals, which were mainly distributed among intergenic spacers and may cause rearrangement of the mitogenome. The phylogenetic results showed thatCladonia subulataandC.polycarpoideswere assigned to theCladoniaSubclade. The results add to the available mitochondrial genome sequence information ofCladonia subulata, provide basic data for the systematic development, resource protection, and genetic diversity research inCladonia subulata, and also provide theoretical support for further genomic research of lichens.