BACKGROUND: The fact that bats suppress agricultural pests has been measured for some particular dyads of predator and prey species in both economic and food security terms. The recent emergence of new molecular techniques allows for more precise screenings of bat's diet than the traditional visual identification systems and provides further evidence that bats consume an ample array of agricultural pest species. The main focus of the regulatory services that bats provide in agroecosystems has been on crop pests that cause yield losses. Rice paddies constitute a particular agronomic system with specific challenges, not only related to crop productivity but also to human health. Dipteran density in such ecosystems poses a serious threat to human wellbeing and hinders crop production. Mosquitoes cause direct harm to human populations, transmitting a number of infectious diseases. Non-biting midges (Chironomidae) can consume and weaken rice seedlings and can cause major yield losses. RESULTS: Mosquito populations and bat activity were assessed in rice paddies of Montgrí, Medes i Baix Ter Natural Park (NE Iberian Peninsula). Molecular analyses of bats faeces (6-weekly samples of 15 faeces each between mid-August and September) proved the presence of both mosquitoes and nonbiting midges in all diet samples. Furthermore, bat activity at the sampling locations was related to adult mosquito density. CONCLUSION: Our results suggest that bats actively exploit the emergence of adult mosquitoes and further prove that they prey on mosquitoes, nonbiting midges and other deleterious insects. Promoting the presence of bats next to human settlements in such agroecosystems may constitute a biological control system with direct impact on both human health and crop yield.