Dragonflies and damselflies, representing the insect order Odonata, are among the earliest flying insects with living (extant) representatives. However, unravelling details of their long evolutionary history, such as egg laying (oviposition) strategies, is impeded by unresolved phylogenetic relationships, an issue particularly prevalent in damselfly families and fossil lineages. Here we present the first transcriptome-based and AHE-based phylogenetic reconstructions of Odonata representing nearly all of the order’s families (except Austropetaliidae and Neopetaliidae). All damselfly families and most dragonfly families are recovered as monophyletic groups. Our Molecular clock estimates suggest that crown-Zygoptera (damselflies) and -Anisoptera (dragonflies) both arose during the late Triassic. Similarly, Dictyoptera analyses are resolved with AHE phylogenetic reconstruction.