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<i>Ganoderma</i> species are widely distributed in the world with high diversity. Some species are considered to be pathogenic fungi while others are used as traditional medicine in Asia. In this study, we sequenced and assembled four <i>Ganoderma</i> complete mitogenomes, including <i>G. subamboinense</i> s118, <i>G. lucidum</i> s37, <i>G. lingzhi</i> s62, and <i>G. lingzhi</i> s74. The sizes of the four mitogenomes ranged from 50,603 to 73,416 bp. All <i>Ganoderma</i> specimens had a full set of core protein-coding genes (PCGs), and the <i>rps3</i> gene of <i>Ganoderma</i> species was detected to be under positive or relaxed selection. We found that the non-conserved PCGs, which encode RNA polymerases, DNA polymerases, homing endonucleases, and unknown functional proteins, are dynamic within and between <i>Ganoderma</i> species. Introns were thought to be the main contributing factor in <i>Ganoderma</i> mitogenome size variation (<i>p</i> < 0.01). Frequent intron loss/gain events were detected within and between <i>Ganoderma</i> species. The mitogenome of <i>G. lucidum</i> s26 gained intron P637 in the <i>cox3</i> gene compared with the other two <i>G. lucidum</i> mitogenomes. In addition, some rare introns in <i>Ganoderma</i> were detected in distinct Basidiomycetes, indicating potential gene transfer events. Comparative mitogenomic analysis revealed that gene arrangements also varied within and between <i>Ganoderma</i> mitogenomes. Using maximum likelihood and Bayesian inference methods with a combined mitochondrial gene dataset, phylogenetic analyses generated identical, well-supported tree topologies for 71 <i>Agaricomycetes</i> species. This study reveals intraspecific and interspecific variations of the <i>Ganoderma</i> mitogenomes, which promotes the understanding of the origin, evolution, and genetic diversity of <i>Ganoderma</i> species.