-Identification of honey bee (Apis mellifera) subspecies is important for their protection. It is also used by queen breeders to maintain some breeding lines. In this study, we compared three methods of subspecies identification based on the following: 17 microsatellite loci, COI-COII mitotypes and geometric morphometrics of forewing venation. The methods were used to classify colonies and workers from a mixed population of A. m. mellifera and A. m. carnica. There was highly significant correlation between results obtained using the three methods. More than three quarters of colonies were classified to the same subspecies by all three methods. The agreement was highest between microsatellites and morphometrics. More than 90 % of colonies were classified to the same subspecies by the two methods. There was also relatively high agreement (75 %) between microsatellites and morphometrics when workers were classified as pure subspecies or hybrids. In particular, one pure subspecies was never misclassified as other pure subspecies. The results presented here show that morphometrics can be used for detection of hybrids between A. m. mellifera and A. m. carnica. geometric morphometrics / subspecies discrimination / microsatellites / mtDNA / Bayesian clustering / Apis mellifera / phenotype-genotype correlation