Larvae of the eastern tree hole mosquito, Ochlerotatus triseriatus, and related container breeding species are known to feed upon substrate-associated microorganisms. Although the importance of these microbial resources to larval growth has been established, there is almost nothing known about the taxonomic composition and dynamics of these critical microbial food sources. We examined bacterial and fungal community compositional changes on oak leaves tethered in natural tree hole habitats of Oc. triseriatus. We eliminated larvae experimentally in a subset of the tree holes and examined 16S rDNA gene sequences for bacteria and 18S-28S internal transcribed spacer region (ITS) sequences for fungi collected from leaf material subsamples. Principal component analysis was used to compare microbial taxonomic patterns found in leaves incubated with or without larvae present. We found that larval presence affected both bacterial and fungal groups, primarily those more loosely associated with the leaf surface. Bacterial communities were similar when larvae were present, but varied substantially when larvae were removed, suggesting strong selection by larval feeding for particular taxa. Fungal taxa composite scores separated along PC axes related to the presence of larvae, also suggestive of selection by larval feeding. These results support the hypothesis that larval mosquito feeding alters microbial composition on substrate surfaces, potentially leading to decreased food value of the resource.