This paper addresses how the design of collaborative regimes influences markers of legitimacy in Swedish water-and large carnivore governance. Based on institutional analysis and statistical analysis of survey data, the study examines two systems with different types of collaborative designs and compares them in relation to markers of legitimacy, in terms of perceived process quality, policy agreement and policy acceptance among the involved decision-making actors and concerned organizations. The findings show how the design of collaboration influences some, but not all, explored markers of legitimacy. First, the categories of actors involved; whom they are accountable to; and the authority given to the collaborative forums, effect perceptions of influence, the possibility of reaching joint agreements and the degree of policy agreement among involved decision-makers. Second, the findings indicate that the degree of policy agreement among concerned organizations is unaffected by differences in institutional design. Third, the degree of policy acceptance among involved decision-making actors and concerned organizations was unaffected by institutional design and notably high in both systems. The results both verify and develop previous research findings and the message to policymakers is to carefully consider the design when introducing new collaborative forums, including whom to invite, in what role, and with what mandate.