The present work aimed to identify camel ticks Hyalomma dromedarii and Hyalomma marginatum using direct sequence of the mitochondrial 16S rRNA gene and the detection of their natural infection rate with Rickettsia and Borrelia using the PCR/ hybridization method for amplification of the citrate synthase (gltA) gene. The phylogenetic analysis showed 99% similarity between Hyalomma dromedarii and its reference with accession # L34306.1, as well as between Hyalomma marginatum and its reference with accession # KT391060.1 obtained from GenBank data base. The prevalence of H. dromedarii and H. marginatum was about 99% and 1%, respectively. The intraspecific variation among H. dromedarii ranged between 0.2-6.6%. The interspecific variation between H. dromedarii and H. marginatum was 18.3%. PCR/hybridization of the sampled H. dromedarii detected about 31%, 37% and 18% natural infection with Rickettsia, Borrelia and co-infection with both pathogens, respectively. In contrast, none of Rickettsia or Borrelia was detected in H. marginatum. The present study emphasizes the accuracy of the identification of camel ticks based on molecular techniques. The ability of H. dromedarii to spread more than one disease is an important issue from the epidemiological standpoint. Future epidemiological research should be carried out in Saudi Arabia to monitor the distribution of tick species and suggest effective control strategies.