In Egypt, tick-borne diseases pose a significant threat to human and animal health, and the threat to dromedaries (Camelus dromedarius), the country's dominant camelid species, is of particular concern. These animals are frequently infested with ticks, and may thus develop tick-borne diseases or become reservoirs of tick-borne pathogens. However, there is a paucity of data on tick infestation in Egyptian camels, especially in the south of the country. Accordingly, we aimed to determine the prevalence of tick infestation in southern Egyptian camel populations (in Luxor and Aswan governorates), and identify the hemoprotozoan parasites carried by camel-infesting ticks. Camels were checked for ticks during veterinary examination at quarantine and household checks, and ticks were collected from infested camels for species identification using morphological examination and PCR analyses. Tick and hemoprotozoan species were identified using Basic Local Alignment Search Tool analysis with subsequent confirmation in phylogenetic analyses. All camel-infesting ticks belonged to the species Hyalomma dromedarii, and were clustered with ticks of this species previously found in Egypt in a phylogenetic tree based on the 16S rRNA gene. Molecular analysis targeting the 18S rRNA gene revealed the presence of hitherto undetected hemoprotozoan parasites, Colpodella spp., in 30/297 (10.1 %) camel-infesting ticks. In phylogenetic analysis, these Colpodella spp. were highly homologous (94–98.6 %) with Colpodella spp. previously deposited in GenBank with accession numbers OQ540590Q, MH208621, and GQ411073, which relate to Colpodella spp. previously detected from Haemaphysalis longicornis, Rhipicephalus haemaphysaloides, and humans in China. PCR analyses with spherical body protein-4 (SBP-4) gene-specific primers revealed Babesia bovis in 16/297 (5 %) of camel-infesting ticks, however, Babesia bigemina and Theileria annulata were not detected. Here, we report the first detection of Colpodella spp. in H. dromedarii in Egypt. Further epidemiological studies are needed to assess the risk to camels and humans, and the transmission dynamics. Based on the high tick infestation rates in Egyptian camels and the identification of previously unreported protozoan hemoparasites in ticks, we consider that the dromedary should be subject to surveillance as a sentinel species for tick-borne diseases in Egypt. Our findings underline the need for surveillance and collecting data on lesser known pathogens circulating in camel-infesting ticks, as part of a public health strategy for dealing with tick-borne diseases in Egypt.