The phylogenetic status and the monophyly of the holometabolous insect order Megaloptera has been an often disputed and long unresolved problem. The present study attempts to infer phylogenetic relationships among three orders, Megaloptera, Neuroptera, and Raphidioptera, within the superorder Neuropterida, based on wing base structure. Cladistic analyses were carried out based on morphological data from both the fore- and hindwing base. A sister relationship between Megaloptera and Neuroptera was recovered, and the monophyly of Megaloptera was corroborated. The division of the order Megaloptera, the traditional higher classification, into Corydalidae (Corydalinae + Chauliodinae) and Sialidae, was also supported by our wing base data analyses.