The pool of microbiota associated with mosquito breeding habitats varies with the habitat type and its characteristic features. The pool of microbiota in a given mosquito breeding habitat can include free living, symbiotic, noncompetitive, parasitic, predatory, and toxin producing species. However, in Sri Lanka the studies on the microbiota associated with mosquito breeding habitats are scarce. The present study was conducted to identify microbiota species/taxa associated with a variety of mosquito breeding habitats in selected areas of the Kurunegala district in Sri Lanka to determine the relationship, if any, the microbiota has with mosquito larvae breeding. A total of 44 microbiota species/taxa belonging to 10 phyla, namely, Bacillariophyta, Charophyta, Chlorophyta, Cyanobacteria/Cyanophyta, Ochrophyta/Heterokontophyta, Amoebozoa, Euglenozoa, Ciliophora, Arthropoda, and Rotifera were identified. Vorticella microstoma (Ciliophora) showed a constant occurrence frequency in rice field habitats occupied mainly by Culex tritaeniorhynchus while the rest of the species had an accidental or rare frequency of occurrence. Nineteen species/taxa were identified as common species. Trophont stages of Vorticella microstoma and Zoothamnium spp. were found attached to the cuticle of mosquito larvae but only V. microstoma caused a lethal effect. The autotrophic protist, Euglena geniculate, Closterium spp., and Pinnularia spp. served as the diet items to mosquito larvae. The majority of the microbiota identified had no observable effect on mosquito larvae breeding.