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In highly developed regions, ecosystems are often severely fragmented, whereas the conservation of biodiversity is highly rated. Regional and local actor groups are often involved in the regional planning, but when making decisions they make insufficient use of scientific knowledge of the ecological system that is being changed. The ecological basis of regional landscape change would be improved if knowledge-based systems tailored to the cyclic process of planning and negotiation and to the expertise of planners, designers and local interest groups were available. If regional development is to be sustainable, goals for biodiversity must be set in relation to the actual and demanded patterns of ecosystems. We infer a set of prerequisites for the effective use of biodiversity goal-setting methods in multi-stakeholder decision making. Among these prerequisites are the requirements that ecosystem patterns are set central and that methods integrate the demands of a suite of species, are spatially explicit, and allow the aspiration level to be modified during the planning process. The decision making must also be enriched with local ecological knowledge. The current methods for setting biodiversity targets lack crucial characteristics - in particular, flexibility - and often require too high a level of ecological expertise. The ecoprofile method we designed combines an ecosystem base with spatial conditions for species metapopulations. We report experiences with this approach in two case studies, showing that the method was understood by policy makers, planners, and stakeholders, and was useful in negotiation processes. We recommend experimenting with applying this approach in a variety of circumstances, to further improve its ecological basis.