Alaska ecosystems face numerous dynamic issues that cannot be adequately addressed at the individual resource management agency or landowner level. In response, the Biological Resources Division of the USGS (formerly the National Biological Survey) initiated in 1994 two ecosystem initiatives in Alaska: the Glacier Bay Ecosystem Initiative and the Prince William Sound/Copper River Ecosystem Initiative. Both were designed to develop ecosystem-based approaches to science & resource management through development of partnerships among resource managers and scientists. Two partnerships have been developed in these areas. The Glacier Bay Ecosystem Partnership has thus far been joined by 7 Federal agencies, 3 State of Alaska agencies, & 2 Native organizations. The Prince William Sound/Copper River Basin Natural and Cultural Resources Cooperative consists thus far of 6 Federal agencies, 3 State of Alaska agencies, and 2 Native organizations. The partnership groups have identified important resource management issues for their agencies in these regions and have started working collaboratively to address these issues and their scientific needs. The next phase of this project will be to develop conceptual ecosystem models as a framework for understanding issues and improving efficiency of research in Glacier Bay, Wrangell-St. Elias, and Denali National Parks and Preserves (NPP). For Denali NPP, the model will provide the foundation for the USGS-funded Prototype Inventory & Monitoring Program. For Wrangell-St. Elias NPP, the model will provide a context for understanding predator-prey relationships affecting populations of important subsistence resources and long-term effects of a major spruce beetle infestation which has killed much of the mature white spruce in the park. For Glacier Bay NPP, the model will be an integral part of monitoring of the Vessel Management Plan, which regulates all ships and boats that enter Park waters (the primary way people visit the Park).