Companion animals can be infested by various species of parasitic insects. Cat flea Ctenocephalides felis (C. felis felis) (Bouché, 1835) and dog flea Ctenocephalides canis (Curtis, 1826) belong to multihost external parasites of mammals, which most frequently occur on domestic cats Felis catus Linnaeus and dogs Canis familiaris Linnaeus. The main aim of this study was to investigate the presence of pathogens, such as Anaplasma phagocytophilum (syn. Ehrlichia phagocytophila) and Rickettsia spp., in adult C. felis and C. canis fleas. Flea sampling has been realised from January 2013 to April 2017 in veterinary clinics, animal shelters and pet grooming salons. Fleas were collected from domestic cats and dogs, directly from the pet skin or hair. Then, the DNA was isolated from a single flea by using the alkaline hydrolysis and samples were screened for the presence of pathogens using PCR method. Anaplasma phagocytophilum has occurred in 29% of examined C. felis and 16% of C. canis individuals. In turn, the prevalence of Rickettsia spp. in cat fleas population was only 3%, and the dog fleas 7%. The present study showed the presence of pathogenic agents in cat and dog fleas, which indicates the potential role of these insects in circulation of A. phagocytophilum and Rickettsia spp. in the natural habitat. Furthermore, exposition to these flea species, whose hosts are domestic cats and dogs, can pose a potential risk of infection for humans.