Nosema is one of the most serious pathogens in honey bees worldwide. It is correlated that infected bees suffer both shortened lifespans and higher winter mortality. The current study aimed to determine the prevalence of Nosema ceranae in Apis florea as a new migratory insect into Egyptian ecosystem. Apis florea samples were collected from seven different regions in Egypt. Apis mellifera was used as a positive control. All samples were examined by using a light microscope and tested by polymerase chain reaction (PCR) device. In addition, all PCR products were further purified and sequenced. Moreover, we performed phylogenetic analyses with the aid of the 16S rRNA gene sequences of Nosema ceranae to elucidate the genetic relatedness between strains isolated from distinct honeybee species. Both microscopic examination and sequencing of PCR products determined the presence of Nosema ceranae in Apis florea. It was observed that several nucleotide' differentiations were found compared to the sequence of Nosema ceranae from Apis mellifera in Egypt. These results may indicate the presence of other species and subspecies of modern or newly introduced pathogens that may be later transmitted to honey bees (Apis mellifera) in Egypt. Therefore, we recommend periodic examination of bees to protect them from transmission diseases and to quickly eliminate any enemies or other pests.