Superfamily relationships within the Hymenoptera have been exceedingly difficult to resolve using conventional morphological and molecular markers. Genomic scale approaches to phylogenetic reconstruction have recently come in vogue to compensate for misleading gene trees and ambiguity found in small gene data sets. To test the utility of using ESTs in Hymenopteran systematics, we sampled 2000 clones from 2 cDNA libraries from Neodiprion sertifer (Diprionidae) and Campoletis sonorenis (Ichneumonidae), resulting in 795 and 761 unique gene clusters, respectively. To discover orthologous genes in other taxa, we compared these sequences with Hymenopteran and other insect ESTs in public databases using stringent criteria. These EST-derived markers were used to build a large concatenated data matrix for a subset of taxa across the Hymenoptera. Results indicated that phylogenomic approaches are fairly robust to method of analysis and have great potential for resolving deep evolutionary divergences within the Hymenoptera. Putative relationships among the Aculeata, Ichneumonoidea, Chalcidoidea and Symphyta are discussed in light of the results. Although taxon sampling is limited, phylogenomic methods can provide a systematic foundation that may be enhanced by more traditional approaches. Furthermore, ESTs offer a great resource for the development of novel genes for systematic analysis.