In this study, we show that the house mouse (Mus musculus) is the most abundant small mammal in the National Reserve of Lachay in central Peru, and that its large population fluctuations are independent of seasonality. Also, we found that M. musculus is the main small mammal prey of burrowing owls (Athene cunicularia) in Lachay, and that owls respond functionally to mouse abundance. In addition, vegetation cover seems to have a strong effect on small mammal predation by burrowing owls, and possibly other predators such as eagles and foxes. We propose the hypothesis that burrowing owls in arid environments can survive several months eating only arthropods, but that their reproduction is synchronized with a highly nutritious diet, provided by small mammal consumption. The principal prediction of this alternative prey hypothesis is now supported by our data from a tropical ecosystem.