The complementary sex determiner (csd) gene determines the sex of the western honey bee (Apis mellifera L.). Bees that are heterozygous at the csd locus develop into females; whereas hemizygous bees develop into males. The co-occurrence of two identical csd alleles in a single diploid genome leads to the genetic death of the bee. Thus, the maintenance of csd diversity in the population is favoured. The number and distribution of csd alleles is particularly interesting in light of the recent decline in the honey bee population. In this study, we analysed the distribution of csd alleles in two Polish populations separated by about 100 km. We analysed the maternal alleles of 193 colonies and found 121 different alleles. We also analysed the distribution and frequency of the alleles, and found that they are distributed unevenly. We show that the methods that have been used so far to estimate the total worldwide number of csd alleles have significantly underestimated their diversity. We also show that the uneven distribution of csd alleles is caused by a large number of infrequent alleles, which most likely results from the fact that these alleles are generated very frequently.