Acanthocephala is a relatively small, but distinct obligate parasitic group that includes 4 classes: Archiacanthocephala, Palaeacanthocephala, Polyacanthocephala, and Eoacanthocephala. The phylogenetic relationships of acanthocephalans are mainly based on nuclear ribosomal genes. In this study, we determined the complete mitochondrial genome sequence of Southwellina hispida (Palaeacanthocephala: Polymorphida), and used this genome sequence along with other platyzoan species (including syndermatan groups) to assess its phylogenetic position within Acanthocephala. The S. hispida mtDNA is a 14,742bp circular molecule that contains 36 genes (lacking atp8) encoded in the same direction. Phylogenetic analyses of amino acid sequences for 12 protein-coding genes suggested palaeacanthocephalan species to be monophyletic, and this group to be sister to Eoacanthocephala. These results confirm other morphological and molecular data supporting palaeacanthocephalan monophyly.