As archipelagic region, an effort to effectively enhance and accelerate the development of each sub-districts to boost the rapid development of Southeast Maluku district in Indonesia cannot happen as long as the local government fails to identify the real potentials and power in fisheries sector of each sub-districts. Identification of each sub-district fisheries top sub-sector has to be based on the human resources, natural resources, infrastructure, current and potential market, current policy of local and central government. A multi-criteria decision making (MCDM) is one of the powerful tools to provide a better result based on complicated factors involved. This paper proposed an integrated MCDM, to tackle the complicated factors in order to provide the best commodities on each sub-districts. Bottom-up concept was used to have a comprehensive result, by combining Fuzzy logic with Analytical Hierarchy Process (AHP) to measure the factors using fuzzy logic with Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) for determining the top sub-sector in fisheries. For comprehensive assessment of macro factors the study used experts ranging from government, scientists, practitioners to NGOs. On the other hand, for micro factors the survey used field instructor, field officer, fishers and farmers. The results provide a guideline for local and central government to form a better policy regarding the development of each sub-district including farmers, fishers and coastal communities in each sub-district to focus on commodities that benefited their regions’ resources and coastal community’s capabilities. By doing so, we hope to contribute on crafting an integrated and collective path on reaching the goal which is the welfare of coastal region.