Higher level systematic studies of the Insecta have yet to firmly resolve the interrelationships of the majority of the insect orders. Attempts to resolve them currently turn on the development of new genetic markers and the collection of extra genetic data for analysis. We have been optimizing the mitochondrial genome for use as a phylogenetic marker both as a collection of individual genes and as a whole genome. Technical limitations to efficient genome sequencing still exist and will be discussed. Use of the whole genome in phylogenetic inference show great promise in resolving relationships but lack of key taxa is currently the greatest challenge facing widespread use. A phylogeny of the insect orders and major suborders based on mitochondrial genome data will be presented.