In the present study, the complete mitogenome of Turbinellus floccosus was sequenced, assembled, and compared with other basidiomycete mitogenomes. The mitogenome of T. floccosus consists of a circular DNA molecule, with a size of 62,846 bp. Gene arrangement analysis indicated that large-scale gene rearrangements occurred in the levels of family and genus of basidiomycete species, and the mitogenome of T. floccosus contained a unique gene order. A significant correlation between the number of introns and the mitochondrial genome size of Basidiomycota were detected (P < 0.01). A total of 896 introns were detected in the core protein-coding genes (PCGs) of 74 basidiomycete species, and the cox1 gene was the largest host gene of basidiomycete introns. Intron position class (Pcls) P383 in the cox1 gene was the most common intron in Basidiomycota, which distributed in 40 of 74 basidiomycete species. In addition, frequent intron loss/gain events were detected in basidiomycete species. More than 50% of bases around insertion sites (- 15 bp to 15 bp) of Pcls from different species were conservative, indicating site preferences of intron insertions in Basidiomycota. Further analysis showed that 76.09% of introns tended to insert downstream to a T base in Basidiomycota. Phylogenetic analysis for 74 basidiomycetes indicated mitochondrial genes are effective molecular markers for phylogeny of basidiomycetes. The study served as the first report on the mitogenome from the family Gomphaceae, which will help to understand the intron origin and evolution in Basidiomycota.