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IntroductionModern understanding of the concept of genetic diversity must include the study of both nuclear and organellar DNA, which differ greatly in terms of their structure, organization, gene content and distribution. This study comprises an analysis of the genetic diversity of the smut fungusSporisorium reilianumf. sp.zeaefrom a mitochondrial perspective. MethodsWhole-genome sequencing data was generated from biological samples ofS. reilianumcollected from different geographical regions. Multiple sequence alignment and gene synteny analysis were performed to further characterize genetic diversity in the context of mitogenomic polymorphisms. ResultsMitochondria of strains collected in China contained unique sequences. The largest unique sequence stretch encompassed a portion ofcox1, a mitochondrial gene encoding one of the subunits that make up complex IV of the mitochondrial electron transport chain. This unique sequence had high percent identity to the mitogenome of the related speciesSporisorium scitamineumandUstilago bromivora. DiscussionThe results of this study hint at potential horizontal gene transfer or mitochondrial genome recombination events during the evolutionary history of basidiomycetes. Additionally, the distinct polymorphic region detected in the Chinese mitogenome provides the ideal foundation to develop a diagnostic method to discern between mitotypes and enhance knowledge on the genetic diversity of this organism.