A large-scale estimate of Holodonata phylogeny through combining morphological and molecular data has yet to be performed for the entire group and higher-level relationships within the group appear questionable. We present the first phylogenetic hypothesis for holodonates based on a combination of molecular and morphological data for the majority of extant and fossil lineages. This is the most comprehensive analysis of higher-level relationships in Holdonata to date. More than 150 morphological characters, based on external morphology, wing venation, and larval characters, were coded for all extant and the majority of fossil lineages. DNA sequence data for six genes (12S rDNA, 16S rDNA, 18S rDNA, 28S rDNA, COII, and Histone 3) were sequenced for all major extant lineages of Odonata and all combined data were analyzed under a parsimony framework. These data provide new insights into the current classification, evolution, and diversification of the holodonates. As well as provide insight into the issues concerning missing data.