Phylogenetic analyses of endoparasitic Acanthocephala based on mitochondrial genomes suggest secondary loss of sensory organs

► We sequenced four new syndermatan mt genomes focusing on acanthocephalan taxa. ► The mt gene order is highly conserved among all major acanthocephalan subtaxa. ► Phylogenetic analyses confidently confirm paraphyletic Eurotatoria. ► Inferred trees suggest loss of lateral sensory organs in some Palaeacanthocephala.