The genus of is a group of important ectomycorrhizal fungi. The overlapping of morphological characteristics often leads to the confusion of species classification. In this study, the mitogenomes of five species were sequenced based on the next-generation sequencing technology, including SCYJ1, , and . These five mitogenomes were all composed of circular DNA molecules, with sizes ranging from 49,480 to 103,090 bp. Intergenic sequences were considered to be the main factor contributing to size variations of mitogenomes. Comparative mitogenomic analysis showed that the introns of the mitogenome experienced frequent loss/gain events. In addition, potential gene transfer was detected between the mitochondrial and nuclear genomes of the five species of . Evolutionary analysis showed that the gene of the species was under positive selection or relaxed selection in the evolutionary process. In addition, large-scale gene rearrangements were detected between some species. Phylogenetic analysis using the Bayesian inference and maximum likelihood methods based on a combined mitochondrial gene set yielded identical and well-supported tree topologies. This study promoted the understanding of the genetics, evolution, and phylogeny of the genus and related species.