Rice fields in Sri Lanka create suitable breeding places for vector mosquitoes. Such sites provide habitats for diversified naturally occurring microbiota. Ciliated protists, Zoothamnium sp., Chilodonella sp., and Vorticella microstoma are among such microbiota found in vector mosquito habitats especially in rice field habitats in Sri Lanka. The present study was carried out to determine the comparative larvicidal effect of these ciliated protists collected from naturally infested mosquito larvae in some rice-field habitats in Kurunegala, Sri Lanka, against vector mosquito larvae. Vector mosquito larvae, Culex tritaeniorhynchus, and Culex gelidus were reared in the laboratory from field-collected water samples while Aedes aegypti mosquito larvae were reared using egg sheets, for the laboratory bioassays. V. microstoma showed the potential for infection and mortality of Cx. tritaeniorhynchus larvae (71.33% ± 5.23). Results revealed a minimum of 1000V. microstoma is required to kill a single third instar larva of Cx. tritaeniorhynchus at 69.60 ± 2.40h of exposure. Cx. gelidus larvae showed 41.33% ± 3.43 mortality due to V. microstoma infestation. However, none of the ciliates were effective against Ae. aegypti larvae. Chilodonella sp. was very occasionally reported during this study hence was not possible to the mass rear for experimentations. This study concludes that V. microstoma is an effective ciliated parasite of Cx. tritaeniorhynchus larvae. Due to their effectiveness and eco-friendly nature, this species can be developed as an effective bio-controlling agent against Cx. tritaeniorhynchus mosquito species.