Ecological genomics (ecogenomics) is a relatively new area of research and innovation, positioned at the crossroads of molecular biology, biotechnology, ecology and soil and environmental sciences. For ecogenomics to contribute to solving complex societal problems, collaboration between scientific and non-scientific actors is crucial. Within the Dutch Ecogenomics Consortium this is addressed by developing and implementing a constructive technology assessment (CTA) approach. In the first step of this CTA approach, guiding visions in ecogenomics were identified. Technology developers were challenged to reflect on the practical implications of their research and the potential value for society. We present the guiding visions and argue that discussing these with other actors (e.g. policy makers and future users) contributes to the development of applications that address societal needs. © 2010 Taylor & Francis.