Aquatic containers, including tree holes and vehicle tires, harbor a diverse assemblage of mosquitoes capable of vectoring important diseases. Many studies have examined containers as a mosquito breeding site, although no data exist that have simultaneously compared mosquito communities between tree holes and tires, and few have quantified differences in environmental factors or food resources that may be important for explaining population or community differences. At two times (early and late summer 2009) we sampled two tire and two tree hole sites in south-central Mississippi, and for each container we enumerated mosquito larvae and measured several environmental parameters (canopy cover, water volume, and detritus), and biomass and productivity of fungi and bacteria, and species richness and abundance of protozoans. Tree holes held less water but were more shaded compared with tires; however, after correcting for volume differences, tree holes contained more detritus and were higher in some microorganism measures (protozoan richness, bacterial productivity in the water column). Based on community dissimilarity analysis of mosquitoes, strong differences existed between container types and sampling period; Aedes albopictus (Skuse) and Culex quinquefasciatus (Say) were dominant in tires, whereas Ae. triseriatus (Say) and Orthopodomyia signifera (Coquillett) were dominant in tree holes. This study also reports the use of tires by the invasive mosquito Cx. coronator (Dyar and Knab). Tree holes supported a higher density of larvae but fewer species than tires, though there was variation across time. Our work illustrates that detrital inputs and some microorganisms differ in fundamental ways between tires and tree holes, and because of compositional differences in mosquito communities, these small aquatic habitats cannot be considered to be homogeneous mosquito habitats.