The phylum Acanthocephala is a small group of endoparasites occurring in the alimentary canal of all major lineages of vertebrates worldwide. In the present study, the complete mitochondrial (mt) genome of Cavisoma magnum (Southwell, 1927) (Palaeacanthocephala: Echinorhynchida) was determined and annotated, the representative of the family Cavisomidae with the characterization of the complete mt genome firstly decoded. The mt genome of this acanthocephalan is 13,594 bp in length, containing 36 genes plus two non-coding regions. The positions of trnV and SNCR (short non-coding region) in the mt genome of C. magnum are different comparing to those of the other acanthocephalan species available in GenBank. Phylogenetic analysis based on amino acid sequences of 12 protein-coding genes using Bayesian inference (BI) supported the class Palaeacanthocephala and its included order Polymorphida to be monophyletic, but rejected monophyly of the order Echinorhynchida. Our phylogenetic results also challenged the validity of the genus Sphaerirostris (Polymorphida: Centrorhynchidae). The novel mt genomic data of C. magnum are very useful for understanding the evolutionary history of this group of parasites and establishing a natural classification of Acanthocephala.