Within systematic biology, there is an increasing emphasis on large-scale, data rich studies, such as the NSF funded ATOL projects. Selecting appropriate molecular markers for phylogenetic estimation remains a critical stumbling block in study design. The difficulties surrounding gene choice become magnified in large-scale projects due to the commitment of time and funding and the lack of precedence in the literature. Gene selection should ideally be based on the ability of genes to accurately resolve relationships among taxa, yet actual choice is rarely evaluated prior to study. Within the Hymenoptera, individual studies have examined the phylogenetic utility of several genes, including some of those selected for the ATOL project, at less-inclusive taxonomic levels, but no study encompass the entire order. I present preliminary data for Hymenoptera relationships among superfamilies based on previously collected data and also an independent test of this hypothesis using nuclear genes. Utility of both ribosomal and mitochondrial genes for large-scale projects such as the Hymenoptera ATOL are also discussed.