The larval stage of culicid mosquitoes are the main food resource of notonectides in aquatic systems. Prey alternation and abundance can significantly affect predator-prey interaction and functional response (FR). We evaluated the effect of predation and prey selectivity of Notonecta peruviana in fourth-stage larvae (F1) of Aedes aegypti and Culex quinquefasciatus at different densities and two test systems: one prey and the combination of both (ratio 1: 1). We used the FR protocol to measure predation and the Manly preference index (αˆi) to evaluate the selectivity of prey, in a CRD experimental design. N. peruviana generated type II RF (“concave model”) of greater impact in larvae of Ae. aegypti (p ≤ 0.01). Predation capacity was similar in both of the prey, 17 ± 4 larvae / day in Cx. quinquefasciatus and 21 ± 4 in Ae. aegypti. The attack coefficient (a), turned out to be similar for both prey species in both test systems and the handling time (Th) was lower for Ae. aegypti than for Culex. Notonecta peruviana demonstrated selectivity for larvae of Ae. aegypti especially at the highest densities (αˆi ≥ 0.5), attributed to the inefficient anti depredation response, active mobility and smaller size compared to those of Cx. quinquefasciatus. The FR demonstrated the success of N. peruviana in the larval control of culicid mosquitoes, prioritizing the type of prey; thus, promoting the need for its applicability in the field.