Using the sterile male technique as an eco-friendly pest control tool has been confirmed in many countries. Therefore, this study was targeted to investigate the genetic divergence of the irradiated wax moth using PCR technique “start codon targeted polymorphism” and draw a phylogenetic tree to find the molecular deviation, which affords a theoretical basis for the efficiency of irradiation as a successful control strategy. This was achieved by exposing the pupae to gamma-ray doses (100; sub sterile and 260Gy; sterile). Exposure of the pupae to radiation caused the presence of new extra bands and the loss of others in SCoT analysis of the emerged adults. A dendrogram was constructed based on the similarity index. It was concluded that the irradiated group with sterile dose was more genetically different than both the control ones and the irradiated group with the sub sterile dose. Conclusions: using SCoT technique could be recommended for differentiation between irradiated and unirradiated moths.