Introduction: Lysinibacillus sphaericus is a highly effective and specific bioinsecticide used for the control of Culicidae larvae. Objective: This study aimed to identify and characterize L. sphaericus strains isolated from Culex quinquefasciatus larvae in Brazil. Methods: C. quinquefasciatus larvae were collected from streams in the urban area of São Paulo state. L. sphaericus strains were identified through cytomorphology, biochemical, and physiological analyses. Qualitative bioassays were performed to evaluate the toxicity of the strains against C. quinquefasciatus. The crystal compound protein pattern of L. sphaericus strains was analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Five reference strains were used as standards in all tests performed. Repetitive extragenic palindromic elements-polymerase chain reaction (REP-PCR) was utilized in an attempt to differentiate pathogenic and nonpathogenic isolates. Results: Twenty-one strains were isolated. Only one presented toxic activity against C. quinquefasciatus. REP-PCR results identified 23 patterns among the 26 strains used in the study, and the fragment analysis showed low similarity (16%) between L. sphaericus isolates and the five reference strains. Conclusion: Comparison of strains isolated in this study using REP-PCR showed a low similarity to other strains, demonstrating the high intraspecific variability for L. sphaericus.