Despite historical and contemporary evidence of its effectiveness, larval source management with insecticides remains little used by most malaria control programs worldwide. Here we show that environmentally safe biological larvicides under field conditions can significantly reduce anopheline larval density in fish farming ponds that have became major larval habitats across the Amazon Basin. Importantly, the primary local malaria vector, Anopheles darlingi Root (Diptera: Culicidae), feeds and rests predominantly outdoors, being little affected by interventions such as long-lasting insecticidal bed net distribution and indoor residual spraying. We found >95% reduction in late-instar density up to 7 d after the first application of VectoMax FG or VectoLex CG (both from Valent BioSciences), and up to 21 d after larvicide reapplication in fish ponds (n = 20) situated in the main residual malaria pocket of Brazil, irrespective of the formulation or dosage (10 or 20 kg/ha) used. These results are consistent with a substantial residual effect upon retreatment and support the use of biological larvicides to reduce the density of anopheline larvae in this and similar settings across the Amazon where larval habitats are readily identified and accessible.