Phylogenetic relationships among basal hexapod lineages were investigated using molecular sequence data derived from three nuclear genes: elongation factor-1α, RNA polymerase II, and elongation factor-2. Nucleotide and amino acids from 12 hexapods and 22 crustacean outgroups were analyzed using maximum parsimony and maximum likelihood methods. The results support most traditional morphology-based relationships, including monophyly of Hexapoda, Diplura, Insecta, and Pterygota. However, placement of Diplura was unstable. Some analyses placed them as the sister group to Ellipura (Collembola Protura) to form Entognatha. In others, Diplura was recovered as the sister group to Insecta, contrary to the Entognatha hypothesis. The analysis also recovered a monophyletic Thysanura sensu lato (Archaeognatha Zygentoma) as the sister group to Pterygota, a conclusion that is consistent with precladistic notions of hexapod systematics but conflicts with current understanding of morphological evolution. The data were also used to reconstruct divergence times from a Bayesian analysis of sequence changes that also incorporated constraints at several nodes based on our understanding of the fossil record. At one node that was not directly constrained by the fossil record (dictyopteran/orthopteroid divergence), our estimate was inconsistent with fossil evidence, suggesting our results (like those using other dating methods) should be interpreted with caution.