Rotifera and Acanthocephala are generally regarded as separate phyla sharing a basal position among triploblast protostomes. This paper presents the first molecular phylogenetic examination of the relationship of Acanthocephala to all three rotifer classes, Seisonidea, Monogononta, and Bdelloidea. Inclusion of Acanthocephala within Rotifera, probably as a sister-taxon to a clade composed of Bdelloidea and Monogononta (the Eurotatoria), is strongly supported by both parsimony and distance methods, using a region of the nuclear coding gene hsp82. Previous molecular evidence for the inclusion of Acanthocephala in the Rotifera suggested that Acanthocephala is a sister-taxon of Bdelloidea, forming the clade Lemniscea. No support is found for this clade, and evidence is presented that the monogonont rotifer used in those analyses, Brachionus plicatilis, may be evolving in an anomalous manner.