The sister group to the isopod crustaceans remains a controversial proposition. Previous studies have used idealised composite taxa or few exemplars, resulting in confl icting assertions about the placement of the Isopoda among the Malacostraca. A recent morphological study argued for an Amphipoda-Isopoda clade, whereas a molecular study using SSU rDNA (18S) data found other relationships. Within isopods, the morphologically-specialised Phreatoicidea are generally regarded as the earliest-derived taxon, based on their fossil record and several published cladograms. These hypotheses were tested using 18S sequences and 202 morphological characters from 75 exemplars (52 isopods and 23 other malacostracans). The partitions were analysed separately and combined, and the sequence data were analysed using dynamic homology. To find the best sequence substitution, insertion-deletion and gap insertion costs, scores based on fi nding accepted monophyletic taxa were used to select the optimal parameters. Separately and combined, both partitions rejected the Amphipoda-Isopoda
clade hypothesis. The 18S analysis placed the phreatoicideans high in the tree, rather in a basal position. The morphological analysis found a basally branching Phreatoicidea-Asellota group. The combined analysis found an Apseudomorpha (Tanaidacea) + Isopoda clade, with Phreatoicidea still well separated from the isopod ancestral root. The parasitic subgroups of the Cymothoida (families Cymothoidae and Gnathiidae, and superfamily Bopyroidea) comprised the basal branch of the isopods, which is a novel hypothesis that argues against the monophyly of the suborder Cymothoida. The 18S data alone are inadequate at this phylogenetic level and the combined data provided novel hypotheses that require additional evidence from detailed morphological studies and DNA markers for confi rmation.