Vector Borne Diseases (VBDs) are considered emerging and re-emerging diseases that represent a global burden. The aim of this study was to explore and characterize vector-borne pathogens in different domestic animal hosts in Egypt. A total of 557 blood samples were collected from different animals using a convenience sampling strategy (203 dogs, 149 camels, 88 cattle, 26 buffaloes, 58 sheep and 33 goats). All samples were tested for multiple pathogens using quantitative PCR and standard PCR coupled with sequencing. We identifiedTheileria annulataandBabesia bigeminain cattle (15.9 and 1.1%, respectively),T.ovisin sheep and buffaloes (8.6 and 7.7%, respectively) andBa.canisin dogs (0.5%) as well asAnaplasma marginalein cattle, sheep and camels (20.4, 3.4 and 0.7%, respectively) andCoxiella burnetiiin sheep and goats (1.7 and 3%; respectively). New genotypes ofAn.centrale,An.ovis,An.platys-like andBorrelia theileriwere found in cattle (1.1,3.4, 3.4 and 3.4%, respectively),An.platys-like in buffaloes (7.7%),An.marginale,An.ovis,An.platys-like andBo.theileriin sheep (3.4, 1.7, 1.7 and 3.4%, respectively),An.platys,An.platys-like andSetaria digitatain camels (0.7, 5.4 and 0.7%, respectively) andRickettsia africae-like,An.platys,Dirofilaria repensandAcanthocheilonema reconditumin dogs (1.5, 3.4, 1 and 0.5%, respectively). Co-infections were found in cattle, sheep and dogs (5.7, 1.7, 0.5%, respectively). For the first time, we have demonstrated the presence of several vector-borne zoonoses in the blood of domestic animals in Egypt. Dogs and ruminants seem to play a significant role in the epidemiological cycle of VBDs.