Despite Amazonia possessing the highest freshwater biodiversity on Earth, urban landing data show how huge fishing pressure is placed on only a dozen species. However, truly characterising the fishery and understanding the drivers of species selectivity is challenging, given the neglect of artisanal fishing activity, who may catch most of the Amazon’s fish. We register the catch of 824 fishing trips by interviewing artisanal fishers in their rural riverside communities. We use these data to characterise the artisanal fishery of the Rio Purus, the main fish source sub-system for the Amazon’s largest city (Manaus), and investigate the factors determining catch composition. Fishers caught 80 fish species, yet just four species made up over half of the harvested biomass. Urban markets appear to drive greater selectivity, with a significantly lower species diversity in commercial compared to subsistence catches. Fish catch composition varied significantly both seasonally and with geographical remoteness from Manaus. The spatial turnover in catch composition appears to be driven by urban access, with more commercially important species dominating where Manaus-based fish-buyers frequent. Our data may partially explain observed overfishing in some commercially important species, particularly as most Amazonians now live in urban areas.