Lysinibacillus sphaericus (Bacillales: Planococcaceae) is a spore-forming bacillus used for the biological control of mosquitoes (Diptera: Culicidae) due to its larvicidal activity determined by various toxins and S-layer protein produced either during sporulation or by the vegetative cell. Aedes aegypti and Culex quinquefasciatus are the vectors of arboviruses that cause tropical diseases representing a current public health problem. Both species may coexist in the same larval development sites and are susceptible to the larvicidal activity of L. sphaericus. In this study, we compared the larvicidal effects of L. sphaericus 2362 (WHO Reference strain) and native strains III(3)7 and OT4b.25 against Cx. quinquefasciatus and Ae. aegypti in single-species and mixed-culture bioassays. Findings showed that L. sphaericus spores, vegetative cells and a combination thereof possessed high larvicidal activity against Cx. quinquefasciatus larvae, whereas only the formulation of L. sphaericus vegetative cells was effective against Ae. aegypti larvae. Similar results were obtained for field-collected larvae. We propose that a formulation of vegetative cells of L. sphaericus 2362 or III(3)7 could be a good alternative to chemical insecticides for the in situ control of mixed populations of Ae. aegypti and Cx. quinquefasciatus.