Abstract: Selecting marine ecological redline is an important part of current marine ecological civilization construction, and the important marine eco-function areas are the key of marine ecological redline,methodology of selecting important marine eco-function areas are still in the stage of exploration. In this paper, the concept and connotation of important marine eco-function areas were proposed, and the methodology used in selecting important marine eco-function areas were analyzed in four steps:first, data collection and ecological features analysis. Second, 9 types of potential important marine eco-function areas were identified in accordance with marine ecosystem services value and important marine ecosystems in the laws and regulations. Third, assessment index system of significance of marine ecological function were established. Fourth, determining boundary of 9 types of important marine eco-function areas in accordance with biogeographic classification principle. Case study was carried out in Quanzhou bay to verify this method.5 types of 10 important marine eco-function areas were identified and the areas are account for 50.28%。