The origin and early diversification of flowering plants (angiosperms) had profound impacts on Earth's biota, providing the raw genetic material from which most crops and economically important plants were derived. The diversification of genes, genomes, and important traits cannot be adequately interpreted without a comparative framework firmly rooted with genome sequences from basal angiosperms. As the sister species to all other extant flowering plants, Amborella trichopoda holds a singular position in the flowering tree of life for establishing this comparative genomics framework. The Amborella Genome Sequencing Project is an NSF funded collaborative project that seeks to produce a high quality finished genome sequence, complete with an accurate chromosome-scale physical map and evidence based gene and transposable element annotations. We are combining the latest multi-platform sequencing technologies with traditional and cutting-edge physical mapping techniques and emerging multi-faceted assembly algorithms to produce a high-quality reference sequence ideally suited for comparative evolutionary analyses to shed light on genomic characteristics of the last common ancestor of extant angiosperms and the evolution of gene content and genome structure throughout angiosperm history. To leverage this genome sequence, we are also developing new bioinformatic tools and a public access website to make this important resource available to the scientific community.