Fungi are a diverse group of organisms with complex mitochondrial genomes and poorly resolved taxonomic schemes. This study examined the utility of concatenated mitochondrial amino acid sequences for inferring fungal phylogenies. Phylogenetic trees generated, supported existing taxonomic proposals based on the analysis of nuclear genes. This study also examined complex introns within Ophiostoma ips strains embedded in the cob and cox3 genes. Fifty-six strains were examined and 11 were selected for sequence analysis. The O. ips cob-490 intron was noted to be composed of three components, two group I intron are situated side by side and one group II intron is nested within the first group I intron. The cox3-640 intron was noted to be a side-by-side twintron composed of two group I introns located next to each other. These introns in part demonstrate why fungal mtDNAs are variable in size and complex in their architecture.