The family Colocongridae and the genus Thalassenchelys are two enigmatic anguilliform taxa whose phylogenetic affinities are poorly understood. Here we present results from parsimony and Bayesian phylogenetic analyses of mitochondrial ribosomal RNA sequences from a taxonomic sample designed to test alternative placements of colocongrids and Thalassenchelys among anguilliforms. The phylogenetic analysis invariably and robustly supports a clade composed of Coloconger and Thalassenchelys, which, in turn, is supported as most closely related to the derichthyids. The degree of DNA sequence divergence observed between Coloconger and Thalassenchelys is comparable to that observed between congeners in the genus Ophichthus and lower than that observed between two members of the subfamily Muraeninae. Because no evidence has been offered to support an alternative placement of Thalassenchelys, we propose that it be included in the Colocongridae. In addition, the results of the present study are congruent with recent molecular-based hypotheses that suggest a close relationship between Anguillidae, Serrivomeridae, and Nemichthyidae, and a monophyletic group comprised of the families Congridae, Ophichthidae, Colocongridae, Derichthyidae, Muraenesocidae, and Nettastomatidae. We found no support for the three major anguilliform lineages that have been proposed based on morphology.