While there has been a global proliferation of marine certification schemes aiming to incentivize sustainable fishing in the last decade, the uptake has been comparatively slow in Japan. Suggested reasons include difficulties assessing Japanese fisheries co-management institutions, and reduced profitability from complex seafood distribution networks and mismatched consumer preferences. However, a few Japanese fisheries have been awarded the international Marine Stewardship Council (MSC) certification. This paper investigates the motivations and experiences of three such MSC applicants: the Kyoto Danish Seine Fisheries Federation offshore fishery, Ishihara Marine Products skipjack and albacore pole and line fishery, and Maruto Suisan rope grown Pacific oyster fishery. Semi-structured interviews were conducted with key informants from each case study and coded into motivations, problems and impacts. It was found that although there were economic motivations to apply for the certification, this mainly involved increasing domestic distribution channels rather than gaining or retaining access to premium-paying foreign markets. The co-management system that governs the Kyoto fisheries hampered the re-certification process of the fishery due to the difficulty of influencing the higher levels of management within the system. It also became clear that the type of applicant was important to consider: the two more recent MSC clients - both seafood processors - are better placed in the value chain to utilize the certification and its logo, and therefore more likely to financially sustain the certification. The study provides an important insight into the applicant experience of certification schemes in countries with lower consumer demand for them, such as Japan.