Marine environments are experiencing intense pressures from anthropogenic activities and climate change, management tools or decision support systems are needed to deal with these problems.The classification of marine habitats is the basis and critical to the protection of marine biodiversity and the sustainable usage of marine resources. The identification of ecologically and biologically significant areas(EBSAs)as a objective,scientific and flexible habitat classification and evaluation tool has been widely accepted by the scientists and managers.The present paper began with the introduction of the progress in the concept and identification method of the EBSAs. Then we developed a protocol and a suite of criteria and indicators to identify EBSAs.Finally,application of the methods to Huanghe River Estuary and its adjacent area is presented as a case study based on the integration of all available ecological information we collected.This study is the first trial of EBSAs identification in China coastal areas.The results of our study are expected to provide scientific methods and tools to the ecosystem-based management and provide references to its applications in other areas.