Abstract Fish in the upper Madeira River basin (Bolivian Amazon) are an important source of livelihoods and protein for both rural and urban human populations. We characterised fisheries in the area of the port city of Riberalta, which possesses some of the most important fisheries landing sites bordering the Moxos lowlands, and evaluated the contribution of an invasive species ( Arapaima gigas ) to the landings. We compared the regional economic contribution of urban‐based and rural indigenous fisheries. Both fisheries contribute significantly to local food security and livelihoods and take advantage in a different but complementary way of the abundance of the invasive species, avoiding conflicts by partitioning the fish catch and supplying different urban markets. Both fisher groups are involved in a debt peonage system making them dependent on middlemen. A. gigas represented 57.6% of the overall economic value of fish in the region. The socioeconomic impact of the invasive species might increase considerably if it would invade and colonise the available habitats in the nuclear area of the Moxos lowlands.