Bartonella spp. prevalence in small mammals and their ectoparasites was investigated in Taiwan. Blood samples were obtained from 66 rats, 20 shrews, 276 mites (Laelaps spp.), 74 fleas (Xenopsylla cheopis), 81 lice (Polyplax spp.), and 47 ticks (41 Dermacentor spp. and 6 Ixodes spp.). Bartonellae were isolated or detected in 27 (31.4%) animals. Bartonella DNA was detected in 48 (64.9%) fleas and 11 (64.7%) pooled lice samples, but not in mite and tick samples. Bartonella phoceensis, B. queenslandensis, B. tribocorum, B. elizabethae, and B. rattimassiliensis were isolated or detected in bacteremic mammals. For the first time in Taiwan, B. tribocorum, B. elizabethae, B. queenslandensis, and a B. rochalimae-like strain were detected in fleas, and B. tribocorum, B. phoceensis, and B. rattimassiliensis were detected in lice obtained from small mammals. A broader range of Bartonella species was identified in the ectoparasites than in the small mammals.