Orthonectids are a group of highly simplified worm-like parasites that are placed within Lophotrochozoa by multigene mitochondrial and nuclear phylogenies. However, their exact position within Lophotrochozoa is uncertain due to the high rate of molecular evolution and putative long branch attraction artifacts. To examine the phylogenetic placement of orthonectids, we applied an alternative approach that takes into account rare evolutionary events (gene order rearrangements in mitochondrial DNA and individual changes in mitochondrial proteins) with an assessment of their probabilities based on a reference sequence database (RefSeq, NCBI). This approach strongly supports the branching of orthonectids among annelids, but does not conclusively resolve their position among the annelid taxa.