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The increasingly complex nature of marine resource management calls for stronger stakeholder participation in advancing knowledge and developing management approaches. Studies on stakeholder involvement in marine resource management have primarily focussed on participation in resource use negotiation and not on participation in science. Using fishers' knowledge research frameworks, we evaluate over 15 years of science-industry research collaboration (SIRC) in Dutch demersal fisheries. Four key lessons emerge: (a) Capacity building in SIRC works multiple ways and triggers shifts in the fishers' knowledge research spectrum; (b) Successful SIRC depends on acceptance of industry collected data for scientific advice, which necessitates close involvement of end-users from the outset to provide feedback and obtain support; (c) (Fisher) participation raises often-overlooked equity questions and may result in selection bias; and (d) The governance context strongly influences structure of SIRC and integration of SIRC knowledge. To ensure a sustainable, continuous process of stakeholder participation and use of their knowledge in marine resources research, collaborative research should be embedded in the institutional frameworks for science and management. It demands continuous maintenance of the relationship between scientists and stakeholders in the context of management developments, calls for reflection about selection and equity considerations, and requires continuous attention for communication with all parties involved at different levels. The lessons learnt in science-industry research collaboration in fisheries are also relevant for the wider field of marine science, where stakeholder participation is necessary but not yet common.