The current understanding of fern phylogeny is primarily based on plastid and nuclear sequences, but the third genome—the mitogenome—has remained practically unstudied. We inferred the first broad scale fern phylogeny based on mitogenomic data, obtained from the One Thousand Plant Transcriptomes Initiative project, and compared it with the plastid phylogeny. The trees were mostly congruent and corresponded to the current understanding of the fern phylogeny, but we observed different evolutionary patterns between the two genomes. Protein-coding markers located in the plastome had, on average, over two times higher substitution rate than the markers from the mitogenome. The similar rate variation pattern between the genomes in different fern lineages supports the idea that a common mechanism, like life history traits, drives the rates of molecular evolution. The few conflicting nodes we observed have also been difficult to resolve in other studies, suggesting that even genomic data may not suffice to resolve them.