Genomic nucleotide content (usually measured as GC content) varies widely among species, the most extreme (AT-rich) of which is in the mitochondria of yeasts. These extreme genomes provide a unique opportunity to study the evolution of genomic nucleotide landscape. In this study, we sequenced six complete mitogenomes of the Saccharomycodes ludwigii yeast, all of which have <10% GC content. Our comparative genomics analyses observed variable intron presence/absence patterns in the large ribosomal subunit (rnl) gene and cytochrome c oxidase subunit I (cox1) gene, and variable lengths of AT-rich tandem repeats. The whole genome alignments among these mitogenomes showed mosaic sequence patterns, suggesting perhaps frequent mitochondrial DNA recombination. We found no evidence of accelerated substitution rates in these Saccharomycodes ludwigii mitogenomes, when compared against other yeast mitogenomes. Thus, mutational pressure and reduced recombination, both of which can lead to increased AT content, are unlikely the main driving force leading to the extreme AT mitogenomes in Saccharomycodes ludwigii. We tend to believe that the proliferation of AT-rich tandem repeats via replication slippage and/or unequal crossing-over plays an important role in driving the extreme AT richness in these mitogenomes.