Here we aimed to create a model of seaweed agro-industry development in the Southeast Maluku district of Indonesia. Data collected from respondents (n = 250) included information related to agro-seaweed, seaweed farming, and seaweed product marketing. Data collection included primary and secondary data sources, while the methods of analysis used structure model equations. We tested eight factors that influence the development of agro-seaweed industries in the southeast Maluku regency, namely, raw materials, human resources, technology, markets, infrastructure, policy, institutional, and capital, and concluded that all proposed hypotheses are proved correct because the value critical ratio ≥ 1.96, only the facilities and infrastructure factors were identified as significantly affecting the development of an agro-seaweed facility in southeast Maluku. We also found that optimal development of an agro-business in southeast Maluku will depend on relevant local government support and require cooperation between the internal local government, academia, the private sector, and the public. Development of human resources through formal and informal education programs directed at local business and focused on seaweed-based products will help to build business continuity by avoiding collusion and nepotism. Increased cooperation will also be required between government, employers, and the fishery community to monitor the sustainability and environmental impacts of the seaweed agro-industry in this region.