The first comparison of the intertidal fish fauna from three estuaries within the longest contiguous mangrove area of the world, in north Brazil, revealed a significant heterogeneity in the species composition and functional and ecological guilds with an increase of Tetraodontidae and Engraulidae and a decrease of Sciaenidae and Mugilidae towards the Amazon mouth. A classification of the mangrove estuaries to identify types of estuaries and coastal sectors is urgently required to provide a tool for regional management systems in order to improve research, monitoring and conservation of this unique mangrove ecosystem.