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Background  Based on previous studies, it was suspected that the mitochondrial  rns  gene within the Ophiostomatales is rich in introns. This study focused on a collection of strains representing  Ophiostoma piliferum ,  Ophiostoma pluriannulatum  and related species that cause blue-stain; these fungi colonize the sapwood of trees and impart a dark stain. This reduces the value of the lumber. The goal was to examine the mtDNA  rns  intron landscape for these important blue stain fungi in order to facilitate future annotation of mitochondrial genomes (mtDNA) and to potentially identify mtDNA introns that can encode homing endonucleases which may have applications in biotechnology.    Results  Comparative sequence analysis identified five intron insertion sites among the ophiostomatoid fungi examined. Positions mS379 and mS952 harbor group II introns, the mS379 intron encodes a reverse transcriptase, and the mS952 intron encodes a potential homing endonuclease. Positions mS569, mS1224, and mS1247 have group I introns inserted and these encode intact or eroded homing endonuclease open reading frames (ORF). Phylogenetic analysis of the intron ORFs showed that they can be found in the same insertion site in closely and distantly related species.    Conclusions  Based on the molecular markers examined (rDNA internal transcribed spacers and  rns  introns), strains representing  O. pilifera ,  O. pluriannulatum  and  Ophiostoma novae - zelandiae  could not be resolved. Phylogenetic studies suggest that introns are gained and lost and that horizontal transfer could explain the presence of related intron in distantly related fungi. With regard to the mS379 group II intron, this study shows that mitochondrial group II introns and their reverse transcriptases may also follow the life cycle previously proposed for group I introns and their homing endonucleases. This consists of intron invasion, decay of intron ORF, loss of intron, and possible reinvasion.    Electronic supplementary material  The online version of this article (doi:10.1186/s40064-016-3076-6) contains supplementary material, which is available to authorized users.

The diversity of mtDNA rns introns among strains of Ophiostoma piliferum, Ophiostoma pluriannulatum and related species