As a lineage, oomycetes have adapted to a wide range of lifestyles. Although the common ancestor of the group was likely a marine pathogen, extant members inhabit a spectrum from free-living saprobes to obligate biotrophs. The mitochondrial genomes of Achlya hypogyna and Thraustotheca clavata were sequenced to directly compare a facultative parasitic species (A. hypogyna) to a closely related free living saprobe (T. clavata). Both sequenced mitochondrial genomes are circular, with sizes of 46,869 bp for A. hypogyna and 47,381 bp for T. clavata. They share 63 common genes, indicating little influence of lifestyle on gene content, but small differences in total number and order of genes. Achlya hypogyna has a single copy of nad2, whereas T. clavata has one pseudogene (rps7) and two duplicated genes (nad5 and nad2), each with one full and one truncated copy. The genomes encode a total of 29 or 30 tRNAs (A. hypogyna and T. clavata, respectively) for 19 amino acids. Three unidentified open reading frames are conserved, and one is unique to T. clavata. Comparisons of these genomes with published sequences of the closely related Saprolegnia ferax mitochondrial genome, and four other more distantly related oomycetes, reveals no correlation in genome content or architecture with lifestyle.