Objectives: The main causative agent of tick-borne rickettsioses in Siberia is considered to be Rickettsia sibirica; however, only a few cases have been genetically confirmed. Other pathogenic species of Rickettsia have been detected in ixodid ticks in Western Siberia. The aim of this study was to detect the aetiological agents of tick-borne rickettsioses in Western Siberia and compare their clinical manifestations. Methods: A total of 273 blood and 44 cerebrospinal fluid (CSF) samples from 273 patients hospitalized because of tick-transmitted infection in April–September 2016 were examined for the presence of Rickettsia spp., using nested PCR with subsequent sequencing. Results: DNA of Rickettsia spp. was found in samples from 10 patients. The gltA gene fragment sequence analysis revealed R. sibirica DNA in seven patients (blood samples) and Rickettsia raoultii DNA in three patients (two blood and one CSF sample). Most patients infected with R. sibirica showed typical clinical symptoms, including high-grade fever (38.9–39.5°С), myalgia, rash, eschar at the site of the tick bite, and elevated levels of serum aminotransferases. In contrast, patients infected with R. raoultii showed nonspecific symptoms with short-term fever (37.2–37.7°С); one patient had a short episode of meningeal syndrome. Conclusions: We report the first finding of R. raoultii DNA in clinical samples from Russian patients. The clinical manifestations of this rickettsiosis were nonspecific and differed from those caused by R. sibirica.