The sequences of the mitochondrial genomes of the oomycetes Phytophthora ramorum and P. sojae were determined during the course of complete nuclear genome sequencing (Tyler et al., Science, 313:1261,2006). Both mitochondrial genomes are circular mapping, with sizes of 39,314 bp for P. ramorum and 42,977 bp for P. sojae. Each contains a total of 37 recognizable protein-encoding genes, 26 or 25 tRNAs (P. ramorum and P. sojae, respectively) specifying 19 amino acids, six more open reading frames (ORFs) that are conserved, presumably due to functional constraint, across Phytophthora species (P. sojae, P. ramorum, and P. infestans), six ORFs that are unique for P. sojae and one that is unique for P. ramorum. Non-coding regions comprise about 11.5 and 18.4% of the genomes of P. ramorum and P. sojae, respectively. Relative to P. sojae, there is an inverted repeat of 1,150 bp in P. ramorum that includes an unassigned unique ORF, a tRNA gene, and adjacent non-coding sequences, but otherwise the gene order in both species is identical. Comparisons of these genomes with published sequences of the P. infestans mitochondrial genome reveals a number of similarities, but the gene order in P. infestans differed in two adjacent locations due to inversions and specific regions of the genomes exhibited greater divergence than others. For example, the breakpoints for the inversions observed in P. infestans corresponded to regions of high sequence divergence in comparisons between P. ramorum and P. sojae and the location of a hypervariable microsatellite sequence (eight repeats of 24 bp) in the P. sojae genome corresponds to a site of. major length variation in P. infestans. Although the overwhelming majority of each genome is conserved (81-92%), there are a number of genes that evolve more rapidly than others. Some of these rapidly evolving genes appear specific to Phytophthora, arose recently, and future evaluation of their function and the effects of their loss could prove fruitful for understanding the phylogeny of these devastating plant pathogens.