In Taiwan, the history of aquaculture spans over three hundred years and the breakthroughs in the artificial propagation of finfish and shrimp effectively reduced the industries' reliance on wild fry, thereby stabilizing commercial operations and overcoming the barriers for expansion. Taiwan is located very close to Japan, one of the biggest seafood importers in the world, which has also benefited the development of aquaculture. However, the growing problems of water pollution and the increasingly high environmental costs generated by aquaculture ventures have made Taiwan experience a declining trend in recent years. To overcome those constraints, three main areas are described, which then form the basis of this study. (1). Adjustment of existing production practices - Milkfish culture, one of the most vulnerable sectors suffering from price fluctuation is used as an example to understand both the production cost, market attributes and the ways in which impacts of variations between production and price can be reduced. (2). Improving existing systems - One of the methods to reduce the use of underground water is to use super intensive culture in which high densities are stable and water use minimised, and has been tried in Taiwan for eels. However, the cost and benefits must be evaluated and as most eel products are exported to the Japanese market, it is very important to examine the comparative advantages against other countries. (3). Develop new systems- One of the solutions to the constraints of land-based aquaculture in Taiwan is to develop seawater-based cage culture. This has been developed in a limited degree in Ping-Tong and Pen-Hu counties but the feasibility and profitability have not been investigated. Based on 274 milkfish farms, 63 traditional eel farms, 5 intensive eel farms, 22 cage culture farms and 133 consumers from different zones, constituted the primary data, which combined with other secondary data constructed this investigation. The milkfish sector was not economically sound. Farm size in the categories of 4-<5 ha could appear to be more profitable. Cold weather and unstable in price made this industry more risky. The price was very unstable and strongly correlated to seasonal variation of production. The various forms of average financial appraisal have shown that intensive eel culture has a slight advantage over traditional eel culture. However, traditional eel culture has a higher distribution and the financial advantage of intensive culture is primarily due to the cheaper eel seed. The mass production of eel from China has caused Taiwan to lose the comparative advantage in roasted eel for the Japanese market. Cage culture is a new aquaculture venture in Taiwan. The structure of cages, feed and other facilities still need to be improved. Although Dumerils's Amberjack (Seriola dumerili) and red porgy (Pagrus major) can make higher profits than other species, fish farmers still have great expectation for cobia (Rachycentron canadus). As Taiwan's market is not big enough, there is great hope that the Japanese market can be developed and cobia can become a candidate for sashimi (raw fish). For sustainable development, aquaculture must be economically viable, ecologically sound and socially acceptable. To attain these goals, production and marketing groups, and production area were suggested. Proper administration and management could help the industry to be sustainable.