Ecosystem-based management is generally viewed as one of the most promising avenues for addressing the various anthropogenic pressures facing the world’s marine ecosystems. These approaches have been developed to varying degrees by individual countries or international organisations, but there remain a large proportion of marine ecosystems, particularly in developing regions, that have not yet been the subject of such research. In these areas, lack of effective regulation and the often high importance of the marine environment in providing food and economic opportunities, together create conditions where marine resources and habitats come under unsustainable levels of pressure. Here, we present a data-limited assessment approach to discern marine ecological patterns, in this case for the exclusive economic zone of Vietnam. By combining data from environmental and biological surveys from the Vietnamese national survey dataset and local oceanographic models, we have identified a series of 12 candidate ecological production units, delineated by their environmental characteristics, and the key commercial species that exist within them. These units are suggested as a possible foundation for a spatial management structure in the Vietnamese exclusive economic zone including considerations such as placement of marine protected areas, or ecological boundaries of key areas of socio-economic importance.