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Monophyly of the pterygote insects is generally accepted, but the relationships among the three basal branches (Odonata, Ephemeroptera and Neoptera) remain controversial. The traditional view, to separate the pterygote insects in Palaeoptera (Odonata + Ephemeroptera) and Neoptera, based on the ability or inability to fold the wings over the abdomen, has been questioned. Various authors have used different sets of morphological characters in support of all three possible arrangements of the basal pterygote branches. We sequenced 18S and 28S rDNA from 18 species of Odonata, 8 species of Ephemeroptera, 2 species of Neoptera, and 1 species of Archaeognatha in our study. The new sequences, in combination with sequences from GenBank, have been used in a parsimony jackknife analysis resulting in strong support for a monophyletic Palaeoptera. Morphological evidence and the phylogenetic implications for understanding the origin of insect flight are discussed.