Oniscidea is a very large and diversified group of crustaceans. This sub-order of Isopoda includes terrestrial animals only, that is unique among crustaceans. The phylogenetic relationships among isopods remain contradictory despite numerous morphological studies. Debates concern essentially i) the origin of Oniscidea and its relationships with the other sub-orders of aquatic isopods, ii)the relationships between two families, Ligiidae and Tylidae, considered as primitive or recently derived according the authors. To avoid the adaptive convergences observed in morphological characters, we have investigated the phylogeny of Oniscidea using molecular data. Partial sequences of the mitochondrial 16S rRNA gene were obtained from 42 species of aquatic and terrestrial crustaceans from 31 genera. Phylogenetic analyses were performed using the distance, maximum parsimony, and maximum likelihood reconstruction methods and different samplings of crustaceans. This gene provided well supported information notwithstanding the high taxonomic level of this study, indicating a useful amount of variation despite the noise due to multiple substitutions. The phylogenetic inferences demonstrated that (a) Crinocheta and Synocheta sections are monophyletic and sister-groups, (b) Ligiidae and Tylidae representatives are in a basal position compared to other oniscids, (c) Helleria brevicornis the only representative of the Helleriinae subfamily, has undergone evolution different from that of the other terrestrial isopods, (d) the relationships between aquatic isopods and ancient groups of Oniscidea are not resolved, probably due to fast radiation not discriminated by the molecular phylogeny.
