The ability to fly is the decisive factor for the evolutionary success of winged insects (Pterygota). Despite this, very little is known about the ground-pattern and evolution of the functionally very important wing base. Here we use the Ephemeroptera, usually regarded as the most ancient flying insects, as a model for the analysis of the flight musculature and the sclerites of the wing base. Morphology and anatomy of the pterothorax of 13 species of Ephemeroptera and five species of Plecoptera were examined and a detailed description of Habroleptoides confusa (Ephemeroptera: Leptophlebiidae) is given. A new homology of the wing base sclerites in Ephemeroptera is proposed. The wing base of Ephemeroptera possesses three axillary sclerites that are homologous to the first axillary, the second axillary and the third axillary of Neoptera. For example, the third axillary possesses the axillary-pleural muscle that mostly is considered as a characteristic feature of the Neoptera. Many of the muscles and sclerites of the flight system of the Ephemeroptera and Neoptera can be readily homologised. In fact, there are indications that a foldable wing base may be a ground plan feature of pterygote insects and that the non-foldable wing base of the Ephemeroptera is a derived state.