Dromedary camels () are widely distributed in Africa, the Middle East and northern India. In this study, we aimed to detect tick-borne pathogens through investigating prokaryotic and eukaryotic microorganisms in camel blood based on a metagenomic approach and then to characterize potentially pathogenic organisms using traditional molecular techniques. We showed that the bacteria circulating in the blood of camels is dominated by Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria. At the genus level, , , and were the most abundant taxa. Eukaryotic profile was dominated by Fungi, Charophyta and Apicomplexa. At the genus level, was detected in 10 out of 18 samples, while , and were detected in one sample each. Our metagenomic approach was successful in the detection of several pathogens or potential pathogens including sp., , , , -like and uncharacterized sp. For further characterization, we provided the partial sequences of citrate synthase () and heat-shock protein () genes of Anaplasma camelii. We also detected type A using polymerase chain reaction (PCR) targeting the internal transcribed spacer 1 (ITS1) region. This combined metagenomic and traditional approach will contribute to a better understanding of the epidemiology of pathogens including tick-borne bacteria and protozoa in animals.