Fleas are important vectors of several Rickettsia and Bartonella spp. that cause emerging zoonotic diseases worldwide. In this study, 303 fleas collected from domestic dogs and cats in Ethiopia and identified morphologically as Ctenocephalides felis felis, C. canis, Pulex irritans, and Echidnophaga gallinacea were tested for Rickettsia and Bartonella DNA by using molecular methods. Rickettsia felis was detected in 21% of fleas, primarily C. felis, with a similar prevalence in fleas from dogs and cats. A larger proportion of flea-infested dogs (69%) than cats (37%) harbored at least one C. felis infected with R. felis. Rickettsia typhi was not detected. Bartonella henselae DNA was detected in 6% (2 of 34) of C. felis collected from cats. Our study highlights the likelihood of human exposure to R. felis, an emerging agent of spotted fever, and B. henselae, the agent of cat-scratch disease, in urban areas in Ethiopia.