In the present study, in order to investigation genetic diversity and phylogenetic relationships among the Iranian subspecies honey bee populations morphological markers were used. Sampling was carried out during summer 2014 from 20 provinces of Iran (including West Azerbaijan, East Azerbaijan, Ardebil, Kurdistan, Zanjan, Gilan, Mazendaran, Golestan, North Khorasan, Razavi Khorasan, Hamedan, Kermanshah, Ilam, Tehran, Lorestan, Isfahan, Chaharmahal and Bakhtiari, Fars, Kerman and Sistan and Baluchestan provinces). Totally, 2250 young worker honey bees were investigated using 14 morphological characters (including: forewing length, forewing width, hind wing length, hind wing width, A4, D7, G18, proboscis length, cubital index, sternite index, scutellum color, third & forth tergite length, hind leg length, and third tergite color). The results of variance analysis based on nested design and mean comparisons using LSD method showed that there were significant differences (P<0.01) between the provinces for all analyzed morphological traits reflecting the existence of a diversity between them. The results of correlation coefficient analysis between morphological characters showed that significant correlation between most of the triats. Using Principal Component Analysis (PCA) 3 components were identified that explained more than 81.5% of the data variation. Cluster analysis using WARD method based on morphological characters classified samples in 2 groups. One of the groups involved the bees collected from North, Northwest and West parts of Iran, and the second group involved the bees which were collected from Eastern North, Central part and Southern regions of Iran. Also, a dendrogram based on WARD method divided 29 subspecies of honey bee to 5 distinct clusters. The Iranian honey bee subspecies composed a shared clade with subspecies of Eastern Mediterranean, Near East and Eastern parts of Middle East (O branches).