Tomorrow's biofuels derived from renewable resources could include cellulosic ethanol, “next-generation” biofuels such as higher alcohols, and microbial biodiesel. A vital decision common to all of these processes is selecting the most promising microbial strain to put through the strain development process, whether it is for enzyme production, metabolite production, or as a host for heterologous protein expression. We will report on ongoing bioprospecting projects that tap two vast sources of microbes: the Phaff Yeast Culture Collection, and a bioprospecting survey in the rain forest of Indonesia. The Phaff Yeast Culture Collection at the University of California Davis contains over 7,000 yeast cultures belonging to over 700 different species. This is one of the few public yeast collections in the world that offers screening service to industrial and academic partners. Results of prior and ongoing screening projects will be discussed, including identification of yeasts that tolerate high stress conditions, produce higher alcohols, and have high lipid content. The collection is growing through a bioprospecting project in Indonesia, funded through the NIH International Cooperative Biodiversity Groups program. Microbes are being screened for cellulolytic activities and high lipid content.