This study was carried out to determine the crucial external and internal morphological characteristics for evaluating queens in three rearing periods (May, June, and July). Data of 65 queens reared from the local honeybees of the Sanliurfa (Apis mellifera L.) and Anatolian (Apis mellifera anatoliaca) honeybee colonies were used. Discriminant and principal component analyses (PCA) were done for thirty-one external and internal morphological characteristics of queens. The highest weight of the queen at emergence was determined in May for the Sanliurfa queens and in June for the Anatolian queens. The averages in ovary weight and spermathecae diameter of queens were found to be non-significant according to groups and periods. The number of ovarioles of the queens was different according to rearing period. Using the left basitarsus width variable, the Sanliurfa and Anatolian queens were classified correctly to their pre-assigned groups using discriminant analysis (73.8%). According to the result of PCA applied to all variables of queens, nine components explained 81.68% of the total variation. The seven variables in the first principal component were the left basitarsus length, the right hindleg length, the left hindleg length, the right basitarsus length, the left tibial length, the right tibial length, and the left basitarsus width. The forewing and the hindwing characteristics were included in the second principal component, and the number of ovarioles was included in the third principal component. The study shows that genotypes can be discriminated using the hindleg variables, in particular, as well as the internal and external morphological parameters of the queens.