BACKGROUND: Culex quinquefasciatus resistance to the binary toxin from Lysinibacillus sphaericus larvicides can occur because of mutations in the cqm1 gene that prevents the expression of the toxin receptor, Cqm1 ⊍-glucosidase. In a resistant laboratoryselected colony maintained for more than 250 generations, cqm1 REC and cqm1 REC-2 resistance alleles were identified. The major allele initially found, cqm1 REC , became minor and was replaced by cqm1 REC-2 . This study aimed to investigate the features associated with homozygous larvae for each allele to understand the reasons for the allele replacement and to generate knowledge on resistance to microbial larvicides. RESULTS: Homozygous larvae for each allele were compared. Both larvae displayed the same level of resistance to the binary toxin (3500-fold); therefore, a change in phenotype was not the reason for the replacement observed. The lack of Cqm1 expression did not reduce the total specific ⊍-glucosidase activity for homozygous cqm1 REC and cqm1 REC-2 larvae, which were statistically similar to the susceptible strain, using artificial or natural substrates. The expression of eight Cqm1 paralog ⊍-glucosidases was demonstrated in resistant and susceptible larvae. Bioassays in which cqm1 REC or cqm1 REC-2 homozygous larvae were reared under stressful conditions showed that most adults produced were cqm1 REC-2 homozygous (69%). Comparatively, in the offspring of a heterozygous sub-colony reared under optimal conditions for 20 generations, the cqm1 REC allele assumed a higher frequency (0.72). CONCLUSION: Homozygous larvae for each allele exhibited a similar resistant phenotype. However, they presented specific advantages that might favor their selection and can be used in designing resistance management practices.