We developed 12 polymorphic microsatellite loci for the Asian honeybee, Apis cerana using the magnetic particle method. Eight of these 12 were highly polymorphic, having four to seven alleles with an expected heterozygosity of 0.38 to 0.78. The primers also produce polymorphic products in related honeybee species such as Apis nigrocincta. These loci can be used to study parameters associated with genetic structure, such as paternity frequency and worker reproduction.