Technical Abstract: The mitochondrial genomes of the genera Pythium and Phytophthora encode a similar suite of genes but differ from each other by an inverted repeat (IR) in Pythium that can represent approximately 75% of the genome size. While an IR is not usually found in Phytophthora genomes, a small IR was observed in P. ramorum and P. hibernalis (less than 1.5 kb). In an effort to gain a better understanding of the evolutionary forces responsible for sequence divergence in genomes with and without an IR, as well as to clarify the phylogenetic relationships within the individual genera, the mitochondrial genomes of 15 Pythium and 10 Phytophthora species were sequenced. Comparative genomics among species within a genus indicated that certain regions of the genome were more polymorphic than others. In Pythium, the small unique region and adjacent IR sequences was the most polymorphic region. In Phytophthora genomic inversions were observed with many of the rearrangements corresponding to phylogenetic groupings. Intraspecific variation has provided tools for identification of mitochondrial haplotypes in P. ramorum. Gene order differences between the two genera shows promise for the development of genus and species specific molecular markers.