We screened for microorganisms that can be utilized as new host cells for mosquito larvicides. As long persistence in the environment is required of host cells, we examined the bacterial populations in the guts of mosquito larvae collected from natural breeding habitats. Larvae of Aedes aegypti and Culex quinquefasciatus were examined, and Bacillus species, particularly Bacillus cereus, were found to be the dominant bacterial species in their guts. To investigate the relationship between these Bacillus strains and the mosquito larvae, we re-introduced the bacteria into larvae of Aedes aegypti, C. quinquefasciatus and another common mosquito strain, Anopheles dirus. The cell numbers of Bacillus cereus strains Ae10 and Cx5 in the guts were consistent throughout a 7-d period without food supplementation, suggesting that these strains were able to colonize in the guts of the larvae. To confirm this, we introduced a plasmid containing a kanamycin resistance marker into Ae10 and Cx5 and fed these recombinant strains to C. quinquefasciatus larvae. Even when food was supplemented for 7 d, the recombinant strains, particularly Ae10, were still found in the guts. Under similar conditions, B. thuringiensis serovar israelensis c4Q2-72 was hardly detectable after 2 d, while Escherichia coli could not be detected at all. Their stable retention in mosquito larvae guts and the feasibility of genetic manipulation indicates these strains possess high potential as novel host cells for application in mosquito control.