Fish,with the most abundant genus in vertebrates,is one of the most important indicators for stable aquatic ecosystem. With the global climate changes and over-exploitation,fishery resources have been suffered by heavy stresses,particularly in the estuary where human activitiy is frequent. Thus,how to better conserve and manage fish resources is a crucial issue for biologists. However,it is unrealistic to conserve and manage all species at the same time due to the limitation of manpower and material resources. So the endangered and rare species should be protected in priority. The Minjiang River is the largest river in Fujian province with a total length of 541km. With the complex terrain and drastic changes in salinity,the Minjiang River Estuary and adjacent waters is an important breeding,nursery and foraging ground for many estuarine fish species. Fishery resources in this region have been studied by some researchers,and the results have pionted out that the marine fishery resources have been seriously declining,but none of them refered to the protection priority of the fishes. Based on the survey data collected by bottom trawl in the Minjiang River Estuary and adjacent waters during 2006 and 2007, combined with the historical survey and documentary information,an evaluation index system of protection priority for fishes was established,which consisted of three sub-systems: the endangered species system,the genetic value system and the species value system. Meanwhile,the evaluation grade and standard of priority conservation order of different species was determined by expert consultation. In order to overcome the subjective random of weight determination,the information entropy principle was used to determine the objective weights of each index. Furthermore,the ideal point method was introduced to calculate the protection priority of different species. The results showed that Lepturacanthus savala,Dasyatis laevigatus and Scomberomorus niphonius were the species with the highest protection priority in this aquatic ecosystem,so the three species should be firstly considered while planning fish protection area and setting fishing off season, collecting catch statistical data and regulating fishing gear standards. The results provide significant references for the protection of fishes in this region. In the future research,it is necessary to further strengthen the protection of local endemic species and establish more improved evaluation index system and evaluation standards.