In the mitochondrial genomes of the filamentous Ascomycota, aside from the usual ‘core’ set of genes, one can encounter genes encoding for ribosomal protein S3 (rps3), N-acetyltransferase, and in a few instances aminotransferases. Based on a survey using sequence data from various databases, it was observed that these genes can be located within introns or exist as freestanding genes in intergenic regions. Furthermore, they can also be absent from fungal mitochondrial genomes. The rps3 gene is highly conserved among fungal mitochondrial genomes although examples were noted where the mtDNA version of this gene has been translocated into the nuclear genome. The N-acetyltransferase gene was less frequently encountered and may be a more recent import from the nuclear genome. Both genes serve as examples of genetic elements that appear to be capable of ‘cycling’ or mobilizing between introns and intergenic regions and possible between the nuclear and mitochondrial genomes. This ‘cycling’ mechanism is currently not understood but may involve recombination events and/or movement via RNA intermediates.