Geographic information system (GIS), as a powerful spatiotemporal analysis tool, has been applied to marine fisheries since the late 1980s, and which is widely used in the fields of data processing and analysis of fishery conditions, relationship between fishery resources and environment, aquaculture selection, fishery resources assessment, tagging, marine ecosystem and fishing ground forecasting. But GIS in the marine fisheries still faces with great challenges. The information of fishery resources includes not only fishery data and environmental data, but also socialeconomic data which are closely related with fishermen. That is, in the future GIS in marine fishery should be a set of natural resources and environment systems, human systems, social systems and economic systems. Fisheries management and sustainability based marine ecosystem has been a common concern of community and international organizations, and GIS has greater advantages than traditional methods and will further enhances fishery decisionmaking. The applications of GIS in fisheries will focus on: （1） the establishment of the database and data standardization; （2） the design of key essential fish habitat; （3） the definition of marine protected areas; （4） longterm monitoring and management of resources; （5） distribution and migratory of fish specis and 3D analysis of marine environment. Finally, the establishment of GISbased framework for ocean fisheries information system in our country is proposed.