Nine hundred and fifty-two fleas were collected from 148 cats and 133 dogs at 18 widely distributed geographic locations in Germany and France and examined for the presence of six different Bartonella spp. (Bartonella bacilliformis, Bartonella clarridgeiae, Bartonella elizabethae, Bartonella henselae, Bartonella quintana, Bartonella vinsonii subsp. berkhoffii) by PCR. Thirty-five specimens (3.7%) tested positive for either B. henselae (14 positive fleas) or B. clarridgeiae (21 positive fleas). DNA of other Bartonella spp. were not detected. Bartonella clarridgeiae was the dominating species in samples from France (19 out of 22 positive fleas), whereas B. henselae was more frequent in Germany (11 out of 13 positive fleas). With 3.5% (22 out of 632 fleas) in France and 4.1% (13 out of 320 fleas) in Germany, the overall prevalences of pathogen did not vary significantly between the flea populations of both countries. 5.4% of cats in France versus 16.1% of cats from Germany were infested by fleas carrying Bartonella, whereas 9.5% of dogs in France but none of the examined dogs from Germany were infested by Bartonella positive fleas. The molecular evidence of Bartonella infections reveals that agents of zoonotic potential are established in flea populations in Germany and France and that the spectrum of species can vary significantly from country to country.