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Sweden is undergoing an extensive transformation from single species management towards ecosystem-based management. This study analyses the implementation of the new moose management system, focusing on the newly formed partnerships at ecosystem level (the moose management areas) and their potential to ease conflicts between participants and develop into sustainable collaborations that enable ecosystem-based management. Empirical evidence was obtained from semi-structured interviews with involved actors (hunters, landowners, wildlife managers and forest consultants) in five Swedish counties. Several challenges, based on the participants’ abilities, willingness and understanding needed to implement the new management system, were identified. Lack of funding, unclear roles and responsibilities appear to be the most serious issues. If these are not properly solved, then they have the potential to hamper and aggravate the implementation of the new management system, that is, the ecosystem-based management, as well as the partnership arrangement.