This study was conducted to investigate Babesia canis vogeli, B. canis canis, B. canis rossi, B. gibsoni, Hepatozoon canis, Ehrlichia canis and Anaplasma phagocytophilum species, and to determine the molecular characterizations of the isolates in totally 400 whole blood samples of dogs in Kayseri region. According to the Real Time PCR results, the prevalence of E.canis, B.canis canis, B. gibsoni, A. phagocytophilum, H. canis, and B. canis vogeli was detected as 14.5%, 12.0%, 9.0%, 7.8%, 5.3%, and 2.3%, respectively while B.canis rossi was not detected in the examined samples. 182 (89.7%) out of the 400 samples were found to be infected with a single parasite species, and 21 (10.3%) were found to be infected with two species. According to the pairwise comparisons of 18S rRNA gene region of the isolates under B. canis canis, B.canis vogeli and B. gibsoni, 1.4±0.2%, 0.3±0.2%, and 0.9±0.3% genetic distance were detected with the other similar isolates from the world, respectively. Based on the 16S rRNA gene sequence alignments, 100% identity was found among the 3 isolates of E. canis while 0.1% genetic difference was determined with the isolates from the world. With respect to ankA gene region of A. phagocytophilum, 99.8±0.2% identity and 0.9±0.3% genetic difference were found among the 3 isolates obtained from Kayseri region and the isolates from the world, respectively. The 2 H. canis isolates were showed 100% identity to each other and 0.2±0.1% genetic difference were determined with the other isolates from the world with respect to 18S rRNA gene region. In conclusion, the molecular prevalence of tick-borne protozoon and rickettsial infections in dogs in Kayseri region was determined and the molecular characterizations of the obtained isolates were performed by analyzing the various gene regions in this study. All isolates were recorded to GenBank.