Honeybee (Apis mellifera ) populations are usually distinguished using standard morphometric methods, mainly based on multivariate analysis of distances and angles. Recently, geometric morphometrics, another method of statistical analysis of shape, has been developed. This research was conducted on European honeybees in Iran in 2012. Multivariate analysis on hind wings identified significant differences between honeybee populations from different areas and significant differences in centroid size of fore wings in different geographical areas (F = 10.6, p = 0.000). Populations from nine areas were classified using discriminate function analysis based on shape variables of fore and hind wings. Crossvalidation tests based on discriminant functions of front wings correctly classified 68.2% of the colonies, and cross-validation tests based on discriminant functions of hind wings correctly classified 43% of the colonies.