Amaranth is an annual herbaceous crop with C4 photosynthesis that has an upright growth habit in both temperate and tropical climates. The genus Amaranthus includes approximately 60 species, of which 40 are considered native to the Americas. Currently, cultivated amaranth is primarily used as a food substitute or forage. Traditional breeding for food and forage production has existed for decades. However, research into the biochemical composition of Amaranthus cell wall for biomass production is limited. Amaranth has high biomass yield and quality (greater quantities of cellulose than maize and equal to that of switchgrass; lower quantities of lignin than that of switchgrass and Miscanthus), especially in poor quality land and in areas of water deficiency. The role of amaranth as an underexploited plant with promising economic value has also been recognized by the National Academy of Sciences. The American Amaranth Institute (AAI) has been organized to help promote amaranth research and development with other organizations. We screened >100 popular amaranth collections on biomass and grain yield under drought condition. We will analysis transcripttome sequences from drought tolerant and sensitive or lodging resistant and sensitive plants to discover molecular markers in genes that are associated with important traits of interest, such as biomass and grain yield. With the significant decrease of the genome sequence cost, we can easily develop markers to build a reference map for QTL or gene discovery. The associated markers will be powerful tools applied in marker-assist breeding program of amaranth for biomass and feedstock.