Eight microsatellite loci were used to investigate the genetic structure of the giant honeybee (Apis dorsata) population in
northeast India. This species migrates seasonally between summer and winter nesting sites, and queens appear to return to
their previously occupied site. Furthermore, there is a strong tendency for colonies of this species to aggregate at perennially
utilized nesting sites that may be shared by more than 150 colonies. These behavioral features suggest that colonies within
aggregations should be more related than random colonies, but that the long-distance migration could act to minimize
genetic differentiation both between geographical areas and within aggregations. Our genetic study supports these
conjectures arising from natural history. A. dorsata aggregations are comprised of colonies that share more alleles than
expected by chance. Although queens heading neighboring colonies are not close relatives, fixation indices show significant
genetic differentiation among aggregation sites. However, there appears to be sufficient gene flow among aggregations to
prevent high degrees of relatedness developing between colonies within aggregations. The results also suggest that there is
significant population structuring between geographical regions, although the level of structuring caused by aggregation
exceeds the differentiation attributable to geographic region.