Honey bee populations from the island of Cyprus were analyzed using microsatellite and mitochondrial DNA markers. A total of 268 colonies were sampled in Cyprus, at six different locations-Kyrenia, Katydata, Flassou, Alabra, Troulloi, and Alassa-covering a wide area of the island. Results showed that the Cyprian honey bee Apis mellifera cypria could be distinguished from other Apis mellifera subspecies based on a „double pattern“ of mitochondrial DNA belonging to the C1 lineage and microsatellite DNA belonging to the O lineage. All populations were homogeneous, except the population from Kyrenia, probably due to the introduction of queens or colonies belonging to the C2, C6, and M7 lineages.