Canine vector-borne diseases are of great relevance not only regarding animal welfare but also in relation to the One Health concept. Knowledge concerning the most relevant vector-borne pathogens in dogs is scarce and limited to stray dogs in most western African regions, and there is virtually no information about the situation in kept dogs presenting (regularly) to vets. Therefore, the blood samples of 150 owned guard dogs in the Ibadan area—in the southwest of Nigeria—were collected and analyzed for the DNA of Piroplasmida (Babesia, Hepatozoon, Theileria), Filarioidea (e.g., Dirofilaria immitis, Dirofilaria repens), Anaplasmataceae (e.g., Anaplasma, Ehrlichia), Trypanosomatidae (e.g., Leishmania, Trypanosoma), Rickettsia, Bartonella, Borrelia and hemotropic Mycoplasma using molecular methods. Overall, samples from 18 dogs (12%) tested positive for at least one pathogen. Hepatozoon canis (6%) was the most prevalent blood parasite, followed by Babesia rossi (4%). There was a single positive sample each for Babesia vogeli (0.6%) and Anaplasma platys (0.6%). Moreover, one mixed infection with Trypanosoma brucei/evansi and Trypanosoma congolense kilifi was confirmed (0.67%). Generally, the prevalence of vector-borne pathogens in this sample group of owned dogs in southwest Nigeria was lower than in prior studies from the country and in other parts of Africa in total. This leads to the assumption that, firstly, the exact geographical location has a major influence on the incidence of vector-borne diseases, and, secondly, it seems to make a difference if the dogs are owned and, therefore, regularly checked at a veterinary clinic. This study should raise awareness of the importance of routine health check-ups, tick and mosquito prophylaxis, and a well-managed infectious disease control program to prevent vector-borne diseases in canines.