The i5K is an international effort to sequence the genomes of 5,000 arthropod genomes to accelerate our understanding of all areas of arthropod biology, especially where they overlap human interests. At the Baylor College of Medicine Human Genome Sequencing Center, we have built upon our long history of Arthropod sequencing starting with D. melanogaster to propose a pilot project of approximately 50 arthropod genomes. We propose to start 10 genomes in the last quarter of 2011, and each quarter in 2012. We have been working with the i5K committees in all aspects of the process. Here we describe the processes of species selection, optimal line preparation for DNA isolation, library construction, sequence generation, proposed assembly and automated annotation methods. The species chosen are based around a number of themes, including arthropods of medical interest including vectors, agricultural interest, pests and beneficial, urban pests, and representatives of orders not previously sequenced, symbiotic species, blood suckers, and gall formers. As but one example of the usefulness of such an endeavor, we present early work on the genome of Mayetiola destructor the Hessian fly. This genome encodes more than 1,000 short secreted salivary gland proteins (SSSGPs) that most likely play a significant role in plant control during gall formation. The SSSGPs are highly conserved in UTRs, splice sites and secretory signals, but not other protein coding sequences which are significantly diverged. We believe these genes and the molecules they encode are potential pesticide targets, but more excitingly provide a new avenue to understand and manipulate agricultural plants in general.