ceranae and Vairimorpha apis, causing nosemosis. The study focuses on identifying Nosema species precisely and targeting V. ceranae's Rad3-like helicase for control methods in naturally infected apiary in Egypt. Microsporidian spores from adult worker bees were studied using microscopy, Polymerase Chain Reaction (PCR) with species specific primers, and sequencing analysis for comprehensive Nosema species identification. Accurate diagnosis plays a vital role in the implementation of focused control strategies. Subsequently, results revealed that all positive samples belonged to Nosema ceranae, indicating its presence in Egypt's Sharkia Governorate. The study explores V. ceranae's Rad3-like ATP-dependent DNA binding helicase, vital for its DNA replication and repair processes. Inhibiting this enzyme could hinder parasite growth in bees. Computational simulations predict their effectiveness by identifying potential inhibitors for V. ceranae's Rad3-like helicase. This approach aids in finding drug candidates without extensive lab work. Integrating molecular characterization for Nosema sp. identification and analyzing V. ceranae's Rad3-like helicase as a drug target paves the way for precise control against nosemosis. In conclusion, Nosema ceranae presence in Egypt's Sharkia Governorate is confirmed. Microscopy and PCR sequencing offer reliable identification of Nosema spp. Targeting V. ceranae's Rad3-like ATP-dependent DNA binding helicase presents a promising path for future research and drug development against nosemosis. Further, in-silico studies are crucial to identify potential drug candidates with minimal off-target effects on honeybees.