As in agriculture, fisheries sector faces long list of uncertainty and unsustainability in supply of the products. This is due to the great possibility of natural disaster and moral hazard by the actors in fisheries which lead to the instability of value chain on fisheries commodity from downstream to upstream. Thus, a study must be done in order to explore and minimize the disturbance of the stream of value chain in fisheries. This study aims to investigate the attributes playing big role on affecting value chain cooperation among actors in fisheries commodity in Kei Islands. Data mining is used on the study to determine factors playing major roles in smoothing cooperation in value chain of fisheries commodity, with 220 datasets obtained from actors in fisheries micro-enterprises in Kei Islands taken from August to November, 2019. The result shows that, on average, weights of four data mining techniques; namely support vector machine, fast large margin, logistic regression, naïve bayes and generalized linear model all appear to put management as the leading factor that contributes the most for the cooperation of value chain of fisheries commodity in Kei Islands. This finding implicates that management on all micro-enterprises of fisheries business in Kei Islands has to be the main focus, which is mainly related to basic knowledge on conducting cooperation and maintaining relationship among all actors in fisheries sector, therefore, NGO and local government need to step in and play role on educating all actors for better good governance of the business to obtain the great sustainability in the value chain of fisheries commodity in the region.