The objectives of this study were to (1) determine the effects of imported commercial queen bees from different geographical origin subspecies on the morphological variation of native honeybee population of the Turkeli area; and (2) apply a model to identify and predict the use of commercial queens subspecies. Standard classification function, discriminant function, and constant coefficients for 41 morphological characteristics were determined for two geographic Turkish honeybee subspecies (Apis mellifera anatoliaca and A. m. caucasica) used intensively for commercial queen rearing. Then, the morphological characteristics of unknown worker bee samples from the Turkeli area-where commercial queen bee usage is common-were investigated. The model showed that the area was subject to genetic mixing because of commercial queen usage. The subspecies of 15 unknown test samples were predicted with 100% confidence, and the native bees from 25 of 30 samples from the Turkeli area were successfully predicted using the model developed. Using the model proved that there was a commercial queen bee introduction into the Turkeli area, mainly from the A. m. caucasica subspecies.