In line with international frameworks and following the example of other countries, France conducted a national ecosystem services (ES) assessment in 2012. National assessments are intended to be both comprehensive and useful. In practice, these objectives are conflicting and difficult to reach, leading the experts in charge of the assessment to allocate effort according to their own priorities. In the case of the marine part of the French ES assessment, we consulted stakeholders at the national scale to better connect the assessment to the interest of the end-users. We implemented a participatory approach based on a combination of workshops and online questionnaires. We collected stakeholder’s perception of (i) ES bundle; (ii) hierarchization of issues; (iii) specific issues of concern; and (iv) research needs for different types of marine ecosystems and groups of species. The results of the consultation assisted the assessment process in selecting key issues that necessitate in-depth analysis, and identifying discrepancies between stakeholders’ perceptions and the scientific knowledge that need to be addressed. Stakeholders’ perceptions were also mobilized as an additional source of data to inform decision-makers regarding the state of ecosystems and their ES. In the end, this work underlines the importance of stakeholder’s consultation to support ES assessment and provides guidance for its implementation in the future. Our results can also inform research needs to support the conservation of marine ecosystems.