Honey bee swarming is a crucial behavior for the population reproduction of honey bee colonies in early spring and autumn. It is well known that the honey bee reproductive swarming always shows a genetic diversity among the swarmed individuals of specific genes. This type of genetic diversity always occurs for the individuals that naturally swarmed. Twelve honey bee nuclei were used; six from natural and the other six from artificial swarming. For studying the biological activity parameters including; honey, pollen, and brood. Moreover, the hygienic behavior test, queen weight, queen rearing, and ovarioles number were recorded for two years. Moreover, two different molecular techniques were used such as specific PCR and RAPD PCR. The molecular part helps in understanding the genetic diversity developed between swarm's individuals and those artificial ones. Concerning the biological activities; the results illustrated that the swarm nuclei had a highly significant difference compared with the artificial one in the first year, whenever, non-significant differences were observed between the two examined swarms in the second year. Furthermore, molecular differences were obtained assuming these differences back to the corresponding swarming related genes which mostly control some of the defense genes of hygienic and grooming behavior. These results revealed the presence of a tide-relationship between the bees' immune system and their genetic profiles. Thus, recommend leaving the colonies to prepare for a swarming to enhance their production ability and hygienic behavior after distributing the hunting hives in the apiaries to avoid missing colonies.