Significant environmental challenges, including the genetic and physiological effects of environmental pollutants, the rapid spread of invasive species and diseases, the release of transgenic organisms, and the prospect of global climate change, affect our daily lives and the sustainability of ecosystems. Managing these environmental problems will require new approaches that span the biology of genes, organisms, populations, communities and ecosystems. In parallel with these practical concerns is the basic need to study gene functions in their natural context. The Arabidopsis 2010 project, for example, seeks to understand the functions of all 25,000 Arabidopsis genes within a decade, but to do so understanding the role of the environment in determining gene function is essential. A new priority is evident - understanding the interplay of molecular mechanisms with organismal and ecosystem biology. Combining genomic and ecological research perspectives will answer crucial unresolved questions, but will require significant new multidisciplinary resources, infrastructure and training.