A total of 155 fleas collected in 2009 in Lebanon from 16 cats (104 Ctenocephalides felis specimens, 1 C. canis specimen) and 2 dogs (50 C. canis specimens) were tested for the presence of Rickettsia spp. and Bartonella spp. using molecular methods, including real-time quantitative polymerase chain reaction (PCR), regular PCR, and sequencing of amplified PCR products. Rickettsia felis, the agent of the emerging flea-borne spotted fever in humans, was identified in 17 (16%) C. felis cat fleas. Bartonella henselae, an agent of cat scratch disease, was identified in three (2.9%) C. felis. Our results emphasize the potential risk of these emerging flea-borne infections in Lebanon.