There is paucity in the epidemiological screening of a blood parasite of zoonotic importance, Babesia microti (B. microti) in camels in Egypt. Therefore, a total of 142 individuals of one humped camel (Camelus dromedarius) that were bred in Halayeb and Shalateen were examined for infection and subjected to phylogenetic analysis on blood parasite infection with B. microti. PCR assay focusing on the Babesia microti small subunit rRNA (ss-rRNA) gene was used for detection of its prevalence in camels. Phylogenetic analysis revealed the detection of 17 case from a total of 142 cases with an infection rate of 11.97% using nested PCR assays. Moreover, phylogenetic analyses showed that B. microti was genetically related with German strain that is isolated from voles and rats in France. In conclusion,  this is the first evidence of B. microti infection in camels in Egypt with evidence of the role of one-humped camels in sustaining the babesia transmission in Egypt.