Objectives. To determine the circulation of Rickettsia in the years 2010 and 2011 in border locations in four regions of Peru and their clinical epidemiological and molecular characteristics. Materials and Methods. A cross-sectional study was carried out in Tumbes, Tacna, Madre de Dios, and Loreto. Whole blood samples were obtained from participants for culture and indirect immunofluorescence (IIF) testing. The DNA taken from leukocytes and ectoparasite cultures was used, and those genes detected for Rickettsia that were successfully amplified were sequenced and analyzed. Results. A total of 33.8% of those surveyed carried Rickettsia antibodies (21.7% in Loreto, 33.0% in Madre de Dios, 48.2% in Tacna, and 33.3% in Tumbes). Seropositivity was confirmed with IIF in over 40% of isolates. Molecular tests showed the presence of Rickettsia felis in Ctenocephalides felis of dogs and cats in Tacna and a recently reported species for Latin America, Candidatus Rickettsia asemboensis, in fleas of cats and dogs in Loreto, Madre de Dios, and Tacna. Of the population studied, 81.4% reported a history of contact with ectoparasites, 22.6% were asymptomatic, and 27.8% lived in earthen-floored homes without water or drainage. Conclusions. Serological and molecular evidence confirms the circulation of Rickettsia in the border locations studied, with predisposing epidemiological factors. Tests confirm the presence of two species, Rickettsia felis and Candidatus Rickettsia asemboensis, which represent a potential threat to the health of the inhabitants.