Blood, saliva, and nail samples were collected from 54 dogs and 151 cats and analyzed for the presence of Bartonella henselae with a novel nested polymerase chain reaction (PCR) method. Bartonella (B.) henselae was detected in feral cat blood (41.8%), saliva (44.1%), and nail (42.7%) samples. B. henselae was also detected in pet cat blood (33.3%), saliva (43.5%), and nail (29.5%) samples and in pet dog blood (16.6%), saliva (18.5%), and nail (29.6%) samples. Nine samples were infected with B. clarridgeiae and 2 were co-infected with B. henselae and B. clarridgeiae of blood samples of dogs. This report is the first to investigate the prevalence of B. henselae and B. clarridgeiae in dogs and cats in Korea, and suggests that dogs and cats may serve as potential Bartonella reservoirs.