Cat fleas (Ctenocephalides felis [Bouché]) are the primary ectoparasites of dog and cat populations. In this study, we report the monthly population dynamics of Rickettsia felis and Bartonella spp. (two zoonotic pathogens that can cause human disease) in cat fleas collected from dogs and cats in Taipei, Taiwan, from December 2006 to December 2007. Natural R. felis infection in individual cat fleas was assessed by polymerase chain reaction (PCR) using pRF-, ompB-, and gltA-specific primer pairs. Samples positive by PCR were confirmed with DNA sequencing. R. felis was detected in cat fleas year round, and the average infection rate was 21.4% (90 of 420) in 2007. Cat fleas also play an important role in the transmission of Bartonella between reservoirs and other mammalian hosts. In this study, we used primer pairs specific for the Bartonella gltA and rpoB genes to detect Bartonella infections. Of the 420 cat fleas tested, 38 were positive by PCR for Bartonella. Sequence similarities to Bartonella henselae, Bartonella clarridgeiae, and Bartonella koehlerae were observed in 6.2% (26 of 420), 2.1% (9 of 420), and 0.7% (3 of 420) of the fleas, respectively. Based on the pap31 gene sequence, several amplicons of the B. henselae detected in the cat fleas could be subgrouped into three strains: Fizz/CAL-1 (n = 18), Marseille (n = 5), and Houston-1 (n = 3). These results demonstrate that cat fleas infected with R. felis are endemic to Taiwan, and highlight the role of C. felis in Bartonella transmission between reservoirs and other mammal hosts and demonstrate the genetic variability of B. henselae in Taiwan.