Quaking aspen (Populus tremulodies) has the largest geographic distribution of any North American tree and has tremendous ecological, economic, and aesthetic value. Aspen is associated with high levels of plant and wildlife biodiversity, responsible for carbon sequestration, is an important source of fiber and pulp, and a source of wildlife and livestock forage. Aspen is also a good model for understanding defense systems in tress against herbivores. Advances in aspen genetics have been enhanced by the annotation of the poplar genome as well as a suite of new molecular tools, including the aspen transcriptome. Despite these advances, there are still many gaps in our knowledge on the genomic structure of the aspen genome, including a reference sequence and physical map. Recently aspen has experienced high rates extensive crown thinning, branch dieback, and mortality across North America that has been linked to climatic changes. Climate projections suggests substantial habitat loss (up to 94%) and major shifts in genotypic composition over short to moderate timescales. Aspen is also known for its clonality; an aspen clone, “Pando”, that occupies 43.3 ha in central Utah and contains around 47,000 stems is putatively the world's largest organism. There is a high proportion of polyploidy in aspen, with more than half the apsen individuals in western North America and the majority large clones being triploid. These traits make aspen an ideal species for addressing questions about large-scale variation in clonality and polyploidy.