In this study, we compared two different methodologies (standard morphometrics and geometric morphometrics) in order to determine their ability to discriminate the honey bee populations distributed in Iran. In standard morphometrics, four distances and eleven angles were measured from the forewings of different honey bee populations. A total of 18 landmarks were utilized for the geometric morphometrics analysis. All colonies, described by mean of 40 workers, were correctly classified using both methods. In the case of individual wings discrimination, geometric morphometrics was 83.83% successful and standard morphometrics was 52.77% successful while the geometric morphometrics method is much simpler and easier compared to the standard morphometrics. Therefore, the discrimination ability of geometric morphometrics on the honey bee populations was better than standard morphometrics.