The production of food from marine and freshwaters is undergoing a profound revolution—from hunting to farming or from fishing to aquaculture. Fishing and aquaculture exploit and alter the biodiversity on which they are based, each in different but convergent ways. Fishing harvests a much larger range of biodiversity at ecosystem, species and genetic levels than aquaculture. Nearly 400 aquatic species are cultured and more than 5000 species captured in fisheries. Aquaculture and fishing tend to reduce genetic, species and ecosystem diversity, but along different pathways. Fishing reduces genetic and species diversity through selectively removing target individuals with desired characteristics, such as large size, and alters ecosystems. Aquaculture is currently developing across a broad front, using many different species but in inefficient ways. A deliberate program of careful species selection using a broad range of criteria for farming and markets, including food security, should be encouraged, along with research to close the lifecycles of the selected species, improved farm breeds and conservation of germplasm. Aquatic biodiversity for food production receives little policy and management attention but international research provides major support to its sustainable use and conservation.