Fungal mitochondria are variable in size due to the presence of potential mobile elements such as group I and group II introns and homing endonuclease genes (HEGs). In this work the mitochondrial large ribosomal subunit gene (mt-rnl) of Ophiostoma ulmi and related species have been screened for the presence of introns and intron encoded proteins. Five introns have been noted in different regions of the rnl gene of O. ulmi and related species. Based on this rnl survey and rnl data from Genbank, an rnl intron landscape for ascomycetous and basidiomyctous fungi was generated by using bioinformatic based analysis. A total number of 23 possible intron insertion sites were found in the rnl gene of ascomycetous and basidiomycetous fungi. The results also indicate that regions of the rnl gene are more prone to intron invasion then others. The second project dealt with the evolution of mitochondrial ribosomal protein S5 (rps3) gene within the filamentous ascomycetes fungi. Within members of this group of fungi the rps3 gene typically is a component of the mL2449 group I intron but there are free-standing forms of rps3. The study examined if these free standing forms evolved only once due to an as of yet unknown recombination event or if the rps3 gene was transferred from the mL2449 intron to a new mtDNA locus several times during the evolution of the filamentous ascomycetes fungi. The third project was to sequence and characterize the intron and HEG found in the mitochondrial NADH dehydrogenase 4 (nad4) gene of an undescribed species of Pesotum. A 1.4 kb group IC2 intron has been identified in the nad4 gene of Pesotum strain WIN (M)1630. Overall the three studies demonstrate the invasive nature of introns and their associated ORFs and the potential of these introns to influence gene structure and size variation among the fungal mtDNAs.