Spotted fever group (SFG) Rickettsia are zoonotic and emerging pathogens with considerable impact in public and animal health. Greece is an endemic country of diseases caused by SFG Rickettsia. This work aims to evaluate the prevalence of SFG Rickettsia in ticks collected from domestic hosts including sheep, goats and dogs. Several genetic markers for bacterial genes, such as 16S rRNA, ompA, ompB, atpA, gltA, recA, dnaA and dnaK, were amplified and sequenced to accurately classified the rickettsial pathogens in the ticks. Taxonomy and species classification of the Rickettsia was achieved by combining phylogenetic and in silico digestion analysis of the gene sequences obtained. A total of 187 ticks were collected and classified at the species level as Ixodes gibosus, Dermacentor marginatus, Haemaphysalis parva, H. sulcata, H. punctata, Hyalomma scavatum, Rhipicephalus sanguineus, R. bursa and Rhipicephalus sp. The results showed that 7.5% of ticks were infected with at least one SFG Rickettsia including R. massiliae (n = 3), R. slovaca (n = 5), R. raoultii (n = 1) and R. hoogstraalii (n = 5), collected from sheep (n = 4), goats (n = 5) and dogs (n = 3). Molecular analysis revealed the presence of novel genetic variants of R. hoogstraalii (in H. sulcata and H. parva from goat and sheep) and R. raoultii (in D. marginatus from goat). These results proof the presence of SFG Rickettsia in domestic hosts in Greece, and support the need for continued monitoring, surveillance and further analyses of other hosts and study areas.