This study analyzes the secondary data mainly from year 1988 to 1998. First, we use stepwise regression model to determine the input and output variables for the fish market management in Taiwan. Then, Data Envelopment Analysis and Cplex software are applied to find the relative management efficiency for each wholesale fish market. As the result shows that the relative management efficiency of Kaohsiung, Chinshan, Shuoa, Shungli (Yengankang), Wangkong, Chiangchuingkang, Chinku, Shindarkang, Mitwo (Nanliao), Tzekwang (Kertzeliao), and Tungkang fish markets are among the highest. They are the role models for other fish markets.