||In spite of a significant growth in the world organic aquaculture market over the last decade, the development of organic aquaculture in our country is way behind. One major obstacle is insufficient regulatory framework regarding the guidelines for organic aquaculture, certification bodies, and other evolving legislation. Although Council of Agriculture issued a general guidelines for organic aquaculture on May 25, 2010, fish farmers still require a species-specific organic aquaculture guidelines to abide by for practice and production. It has been considered that freshwater clam, oyster, hard clam, shallow-water cultured milkfish have the highest potential to be identified as organic aquaculture products in Taiwan, the feasibility and guidelines for their organic production remained to be studied. National Taiwan Ocean University (NTOU), National Chia-I University (NCU) and National Kaohsiung Marine University (NKMU) conduct this study on freshwater clam, oyster and hard clam, and milkfish, respectively, during November 2010 and March 2011. Update world organic aquaculture guidelines were collected, categorized, and synthesized by NTOU. Three universities held public hearing and extension education on the draft guidelines of their target species and conducted field investigation on the practice and management of the culture of their target species. Finally the guidelines were drafted and would be presented to Fishery Administration Agency for further examination.