Phylogenetic relationships among Syndermata have been extensively debated, mainly because the sister-group of the Acanthocephala has not yet been clearly identified from analyses of morphological and molecular data. Here we conduct phylogenetic analyses on samples from the 4 classes of Acanthocephala (Archiacanthocephala, Eoacanthocephala, Polyacanthocephala, and Palaeacanthocephala) and the 3 Rotifera classes (Bdelloidea, Monogononta, and Seisonidea). We do so using small-subunit (SSU) and large-subunit (LSU) ribosomal DNA and cytochrome c oxidase subunit 1 (cox 1) sequences. These nuclear and mitochondrial DNA sequences were obtained for 27 acanthocephalans, 9 rotifers, and representatives of 6 phyla that were used as outgroups. Maximum parsimony (MP), maximum likelihood (ML), and Bayesian analyses were conducted on the nuclear rDNA(SSU+LSU) and the combined sequence dataset(SSU+LSU+cox 1 genes). Phylogenetic analyses of the combined rDNA and cox 1 data uniformly provided strong support for a clade including rotifers plus acanthocephalans (Syndermata). Strong support was also found for monophyly of Acanthocephala in analyses of the combined dataset or rDNA sequences alone. Within the Acanthocephala the monophyletic grouping of the representatives of each class was strongly supported. Our results depicted Archiacanthocephala as the sister-group to the remaining acanthocephalans. Analyses of the combined dataset recovered a sister-group relationship between Acanthocephala and Bdelloidea by parsimony, likelihood, and Bayesian methods. Support for this clade was generally strong. Alternative topologies that depicted a different rotifer sister-group of Acanthocephala (or monophyly of Rotifera) were significantly worse. In this paraphyletic assemblage of rotifers, the relative positions of Seisonidea and Monogononta to the clade Bdelloidea+Acanthocephala were inconsistent among trees based on different inference methods. These results indicate that Bdelloidea is the free-living sister-group to acanthocephalans, which should prove key for comparative investigations of the morphological, molecular, and ecological changes accompanying the evolution of parasitism.