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A total of 54 wild rabbits captured from southeastern China were examined for Anaplasma phagocytophilum and Borrelia burgdorferi sensu lato by polymerase chain reaction (PCR) assays. One and three samples were positive for A. phagocytophilum and B. burgdorferi, respectively. Sequence analyses of PCR products identified a variant of A. phagocytophilum and a B. garinii genotype. This is the first detection of the two tick-borne agents in Chinese rabbits, the role of which in the maintenance of the agents deserve further investigations.