Capitellidae is a family of marine annelids commonly found in coastal to deep-sea sediments. These annelids are characterized by capillary chaetae at the anterior and long-handled hooks at the posterior part. Although mitochondrial genomes (mtgenomes) are widely used in phylogenetic analyses of invertebrates, their application is limited in many marine annelid families, particularly in Capitellidae. In this study, we obtained complete or nearly complete (except control region) mtgenomes through high-throughput sequencing of eight species across five genera of Capitellidae: Barantolla sp., Capitella teleta, Mediomastus sp., Notodasus sp. A, Notodasus sp. B, Notodasus sp. C, and Notomastus sp. A and Notomastus sp. B. Our results indicate that species from genera with fewer capillary chaetae (Barantolla and Mediomastus) exhibit a relatively conserved mitochondrial gene order, while those from other genera show significant gene order rearrangements. Group II intron in cox1 is found in newly sequenced Notomastus sp. B and Notodasus sp. A & C. Phylogenetic analysis based on the 13 protein-coding genes (PCGs) or 37 mitochondrial genes (mtgenes) revealed three distinct clades for nine capitellid worms with the mtgenome: Clade 1 includes Mediomastus and Barantolla; Clade 2 consists of Notodasus and Capitella; and Clade 3 comprises Notomastus. Notably, Clade 2 is sister to Clade 3, and both form the sister group to Clade 1. In contrast, a phylogenetic tree constructed from nuclear genes (ncgenes; 18S, 28S, and H3) identified Capitella as an early branching clade within Capitellidae. The tree based on 37 mtgenes + ncgenes identified the Capitella as the sister taxon of Notodasus + Notomastus. Additionally, the Ka/Ks ratios of 13 PCGs in Mediomastus and Barantolla were much lower than those in Notodasus or Notomastus. Together, our results indicate different trajectories of mtgenome evolution in the Capitellidae.
