Facilitation of larval mosquito growth in tree hole habitats is associated with the feeding activity of scirtid beetle larvae. Beetle feeding results in the skeletonization of leaf detritus and the associated conversion of coarse particulate organic matter (CPOM) to fine particulate organic matter (FPOM) in the form of small leaf particles and feces. The factors contributing to facilitation of the Eastern treehole mosquito, Ochlerotatus triseriatus, by scirtid beetle larvae were experimentally examined in tree hole-simulating microcosms. Using molecular genetic techniques, we have identified shifts in the microbial community when scirtid beetles co-occur with Ochlerotatus triseriatus. Such shifts suggest beetle feeding facilitates mosquito production indirectly through the microbial community rather than directly through an increase in available FPOM. Quantitative assays revealed an increased level of fungal activity associated with scirtid presence, supporting the hypothesis of increased processing of leaf detrital inputs. Furthermore, these data suggest a comparatively greater importance of fungi over bacteria as a food resource for developing mosquitoes.