The field of Biodiversity and Ecosystem Informatics (BDEI) brings together computer scientists, biologists, natural resource managers, and others who wish to solve real-world challenges while advancing the underlying ecological, computer, and information sciences. The potential for synergies among these disciplines is high, because our need to understand complex, ecosystem-scale processes requires the solution to many groundbreaking technological problems. Fortunately, we are beginning to see increased support for applied computer science and information technology research in the context of environmental problem-solving. In July, 2001, the National Science Foundation (NSF), in collaboration with the United States Geological Survey (USGS), and the National Aeronautics and Space Administration (NASA), invited proposals for high-risk, small-scale planning and incubation activities to catalyze innovation and rapid advances in this new research community. The papers included in this special issue are selected, peer-reviewed summaries from principal investigators involved in this first NSF BDEI effort. These papers provide an overview of this emerging area and remind us that computer and information science and engineering play a crucial role in creating the technologies from which advances in the natural sciences evolve.