The genus of Rickettsia is gram negative bacteria causing rickettsioses and involve mammal hosts and arthropod vectors in their life cycle (lices, mites, ticks, and fleas). Rats were one of rickettsial hosts, and fleas were rat ectoparasites that involve in the transmision from bacteria into humans. Unspecific clinical manifestation and difficulties of laboratory diagnoses caused the information about rickettsioses in humans were still limited. The aim of this study was to detect Rickettsia spp on rat fleas. Rat flea specimens were collected from three seaports of Semarang, Kupang and Maumere. Specimens were analyzed using PCR method by gltA amplification (primer 877F and 1258R). Confirmation of rickettsia species was conducted by sequencing. The results showed percentages of rickettsial infections on rat fleas for Semarang, Kupang, and Maumere were 19%, 61%, and 44%, respectively. Seven samples from eighteen samples sequences confirmed as Rickettsia typhi and the other 11 samples were Bartonella sp. This study was provided additional information about the presence of Rickettsia in 3 seaport in Indonesia and could be initiating rickettsioses surveilans in the regions.