Advances in molecular techniques and the understanding of honey bee (Apis mellifera) genetics have facilitated the study of ecological processes particularly involving mating and colony genetic structure. Here we present the results of one such investigation; the genetic composition of drone congregations in southwest France and the implication of differential contribution of various genotypes on the conservation of an endemic population. We investigated possible spatial and temporal effects on genotype frequencies in four drone congregations located within three kilometers of 26 colonies of the local honey bee population and 44 colonies of the Buckfast hybrid. Drones were sampled from the four DCAs throughout the summer of 2002 and analyzed using maternally inherited mitochondrial DNA. Our results showed significant seasonal differences in drone congregation usage by drones of different genotypes (native and introduced). Drones with mtDNA typical of the C lineage comprised 81.72 ± 9.55% of the drones captured at congregations in June, where as they comprised 31.3 ± 7.16% of the drones captured in July and 10.24 ± 6.69% of the drones sampled August. However, there were no differences in genotype frequencies among these mating sites in any single week, indicating that genotype had no effect on site usage. These results have broad implications for local conservation efforts which attempt to preserve the genetic distinctiveness of native honey bee populations.