SummaryThe effect of supersedure breeding programmes (replacing each queen with her own daughter) on the maintenance of allelic diversity at the sex-determining locus of the honeybee (Apis mellifera) is analysed. In the models considered, the variances of the allele frequency change at the sex locus (close to equilibrium), and at ordinary loci, have a similar general appearance and they are inversely related to the effective population size. This suggests that supersedure breeding programmes affect genetic variation at the two types of loci qualitatively in a similar way. Quantitatively, the allele frequency changes at the sex locus are affected more strongly by selection than by breeding programmes when the number of sex alleles in the population is relatively small. Computer simulations showed that the time required to reduce the number of alleles of a polymorphic locus by one at either the sex locus or other loci is approximately proportional to the effective population size.