Coral reef fish are an important source of food security and income for human coastal populations. They also underpin ecosystem processes vital for the future ability of coral reefs to generate ecological goods and services. Identifying socio-economic drivers behind the exploitation of fish that uphold these key ecosystem processes and the scales at which they operate is therefore critical for successful management. This study addresses this issue by examining the reef-associated fish value chain in Zanzibar, and how it links to functional groups of fish and maturity stage of fish within these groups. Semi-structured interviews with 188 respondents (fishers, traders and hotel staff) involved in the fisheries and trade with reef-associated fish in Zanzibar and participatory observations were used. The trade with reef fish in Zanzibar is a complex structure involving many different agents and this study shows that these different agents exhibit differential preferences regarding fish functional groups and/or maturity stages within these groups. Consequently, both high and low trophic species, as well as small and large fishes are fished and sold, which leaves no refuge for the fish assemblage to escape fishing. When other market agents than fishers have so much influence and there are few alternative income generating activities, it is not possible to put all burden on fishers. Management measures that extend down the value chain to include all market agents as well as their links to ecosystem processes are thus likely to be needed to reach the target of sustainable fisheries.