Biodiversity provides “raw materials” for the food chain and seafood production, and also influences the capacity of ecosystems to perform these and other services. Harvested marine seafood species now exceed 100 million t y -1 and provide about 6% of all protein and 17% of animal protein consumed by humans. These resources include representatives from about nine biologically diverse groups of plants and animals. Fish account for most of the world’s marine catches, of which only 40 species are taken in abundance. Highest primary productivity and the richest fisheries are found within Exclusive Economic Zones (EEZ). This narrow strip (200 nautical mile/370 km wide) is not only the site of coastal “food factories” but also the area associated with heaviest perturbation to the marine environment. Structural redundancy is evident in marine ecosystems, in that many species are interchangeable in the way they characterise assemblage composition. While there is probably functional redundancy within groups, the effects of species loss on ecosystem performance cannot be easily predicted. In particular, the degree to which biodiversity per se is needed for ecosystem services, including seafood/fishery production, is poorly understood. Many human activities, including unsustainable fishing and mariculture, lead to erosion of marine biodiversity. This can undermine the biophysical cornerstones of fisheries and have other undesirable environmental side effects. Of direct concern are “species effects”, in particular the removal of target and non-target fishery species, as well as conservationally important fauna. Equally disrupting but less immediate are “ecosystem effects”, such as fishing down the food web, following a shift from harvested species of high to low trophic level. Physical and biological disturbances from trawl nets and dynamite fishing on coral reefs can also severely impact ecosystem structure and function. “Broadscale” biological and social effects brought about by fishing carry even more far-reaching consequences. For example, fishing itself can change the age at which sexual maturity is reached, thus affecting the reproductive status of the stock. Hence, fishing may be regarded as a mediator of evolution. Social impacts include conflicts over fish prices and policies arising from heavy fishing and inadequate institutional structures. Measures to increase the sustainability of catches and of biodiversity need to be much more tightly coupled. Promising approaches include use of bio-economic indicators and fully protected marine areas. High- and local-level governance options are also examined. Use of expert systems incorporating “fuzzy logic” are providing useful environmental insights in the ASEAN countries and other parts of the world, and have applications in fishery management and biodiversity conservation.