This study has purpose to develop supply chain performance measurement system on sea fishery industry that located on Sadeng Beach, Gunung Kidul, Yogyakarta. Object of the study is the small and medium scale industries. The objective of this study is to capture the key performance indicators (KPIs) and specific indicators, and to develop performance measurement system which is appropriate on the sea fishery industry characteristics. The research was conducted through two main stages. The first stage, is designing the instrument, it is done by collecting indicators form literature (SCOR and agri-food supply chain) and from respondent, selecting appropriate indicators (helped by Marine and Fisheries (DKP) Coast Sadeng), designing dimensions, verifying the dimensions, weighting the indicators so that improvements can be done by focus on bad indicators which are important. Second stage is measuring sea fishery supply chain using the instrument, the results compared with SCOR. This instrument has six dimensions, which are efficiency, flexibility, responsiveness, product quality, process quality, facilities, and government involvement. This instrument measures the performance with results similar to SCOR. However, this instrument considering the involvement of the government, has indicators that has not owned by SCOR and specific indicators of seafish for consumption supply chain. In addition, this instrument can meet the requirements that can not be met by SCOR, i.e. "not only serves for monitoring, but also improvement" because there are weighted data so that more improvements are focus on important indicators but have poor performance and "fit with the corporate culture"