We evaluated the presence of Rickettsia infection among fleas collected on domestic dogs in two Guarani Indian communities in the suburban area of São Paulo Municipality, Brazil. A total of 114 Ctenocephalides felis felis and 47 Ctenocephalides canis were collected from 40 dogs. A total of 41 C. felis felis (36.0%) and 9 C. canis (19.1%) fleas yielded expected bands by PCR, which were all shown by DNA sequencing to be indentical to the corresponding sequence of a fragment of the Rickettsia felis gltA gene deposited in GenBank. The overall prevalence of R. felis was 31.0% (49/161).