Rickettsioses are a group of emerging diseases caused by closely related bacteria. In Sri Lanka, to date, studies have been focused mainly on human subjects. The present study aimed to identify small mammal reservoir hosts and vectors of Rickettsia spp. and Orientia tsutsugamushi in two districts of Sri Lanka. Quantitative-PCR was carried out to detect Rickettsia using citrate synthase gene and Orientia using 47-kD outer membrane protein antigen gene in blood of small rodents and their infested ectoparasites. In both districts ~7.5% blood samples were positive for Rickettsia. Rattus rattus, Bandicota indica and Mus fernandoni were carriers. Three individuals of Suncus murinus, B. indica and Golunda ellioti had only infected ectoparasites. Copies of gltA/100 µL ranged from 133-1.2 × 10 4 in blood and 197-1.9 × 10 7 in ectoparasites. Of small mammals with ectoparasites, 43% had Rickettsia positive ectoparasites. Rhipicephalus haemaphysaloides, Ixodes ceylonensis, Haemaphysalis spinigera, Haemaphysalis spp., Stivalius aporus and Xenopsylla cheopis were positive. All study sites except three had infected small mammals or ectoparasites. All samples were negative for O. tsutsugamushi. This is the first study to report Rickettsia spp. in small mammals and their ectoparasites in Sri Lanka. Haemaphysalis spinigera, I. ceylonensis and S. aporus are new records of vectors for Rickettsia. This is also the first report of endemic M. fernandoni as a carrier of Rickettsia and G. ellioti with Rickettsia infected ectoparasites. Though rickettsiosis is not life threatening in most cases, it can lead to severe or fatal disease in vertebrate animals and humans. Hence, the knowledge of the distribution of said pathogen in the reservoirs is essential to control the disease.