This study aimed (i) to determine the occurrence of vector-borne pathogens (Cytauxzoon felis, Babesia spp., Mycoplasma spp., Rickettsia spp., and Coxiella burnetii) in domestic cats in Türkiye; (ii) to conduct molecular characterization of identified species; (iii) to assess the genetic diversity among identified species in cats reported worldwide. A total of 311 blood samples were collected from animals visiting Ondokuz Mayıs University Veterinary Faculty Animal Hospital for routine checkups, vaccinations, antiparasitic application, and sterilization. Blood samples were analyzed for the presence of targeted pathogens by PCR analysis. Data on domestic cats (age, sex, breed, and living conditions) were recorded, and statistical analyses were performed to identify potential risk factors for infection. Phylogenetic analyses were performed to assess relatedness among detected pathogen isolates worldwide. Out of 311 cats tested, 13.1 % (n = 41) were positive for at least one pathogen, and 0.9 % (n = 3) were found to be co-infected. PCR analyses detected 9.64 % (n = 30) of examined samples infected with Mycoplasma spp., and 3.5 % (n = 11) with C. burnetii. Babesia spp., C. felis, and Rickettsia spp. were not detected. There was no significant statistical difference between the prevalence of any detected pathogen and data of the cats. Sanger sequencing of the 30 positive PCR products identified Candidatus Mycoplasma haemominutum (CMhm) in 50 % (n = 15), Mycoplasma haemofelis (Mhf) in 36.6 % (n = 11), and Candidatus Mycoplasma turicensis (CMt) in 13.3 % (n = 4). Phylogenetic analysis of the Mycoplasma spp. 16S rRNA gene showed two distinct groups: one belonging to the haemominutum group, clustering with CMhm isolates, and the other from the haemofelis group, clustered with Mhf and CMt isolates. Coxiella burnetii IS1111 gene sequences shared high identity and similarity and clustered with isolates from different countries. This is the first report of C. burnetii in domestic cats from Türkiye. Our data provide information on the presence, molecular epidemiology, and genetic characterization of vector-borne pathogens in domestic cat populations in Türkiye. This study highlights the importance of the epidemiology of vector-borne pathogens for effective disease management in cat populations.