Arthropod-borne bacteria can cause a variety of human infectious diseases and have a high diversity of geographic distributions, animal reservoirs, arthropod vectors, and pathogenic properties. Human-biting, questing adult Ixodes persulcatus and Dermacentor reticulatus ticks, as well as mosquitoes and midges from Western Siberia, Russia, were tested for infection with Borrelia, Bartonella, Rickettsia, Anaplasma/Ehrlichia, and Babesia using nested PCR assays with subsequent sequencing. I. persulcatus ticks were found to be infected with Borrelia spp. (39.5 ± 4.5%), Bartonella spp. (37.6 ± 4.3%), Rickettsia tarasevichiae (90.0 ± 4.8%), Anaplasma phagocytophilum (2.4 ± 1.4%), and Ehrlichia muris (8.8 ± 2.5%), whereas D. reticulatus ticks contained DNA of Borrelia spp. (3.6 ± 2.0%), Bartonella spp. (21.4 ± 4.5%), R. tarasevichiae (3.2 ± 3.2%), Rickettsia sp. RpA4 (51.6 ± 9.1%), and Babesia canis canis (3.6 ± 2.0%). Borrelia garinii, B. afzelii, and their mixed infections were observed among I. persulcatus, whereas B. garinii and B. spielmanii DNA were present in samples from D. reticulatus. Surprisingly, only two human pathogens—Bartonella henselae and B. quintana—were found in ixodid ticks in Siberia, despite long-term sample collection and phylogenetic analysis of all known Bartonella species. Moreover, currently both B. henselae and B. quintana, but none of other tick-borne infectious agents studied, were found in mosquitos of the genus Aedes. Bartonella DNA was detected in 1.9 ± 2.1% Aedes cantans mosquitoes but not in samples isolated from mosquitoes of other species including Ae. punctor, Ae. cinereus, and Ae. communis, or in Byssodon maculata midges. Ba. canis canis was the only subspecies found in D. reticulatus, but no Babesia species were observed in I. persulcatus. Thus, both bacterial infection rates and loads for I. persulcatus exceeded those for D. reticulatus and Aedes spp. Considering the large number of ticks implicated in the transmission of bacteria, human exposure to these infectious agents may be more substantial than is currently believed. From 369 patients with clinical manifestations of generalized infection following tick bites, Borrelia DNA was found in 43 plasma samples, Bartonella DNA in 73 blood cell samples, and R. sibirica DNA in a single sample. Molecular typing indicated the prevalence of infection with B. garinii and B. quintana. Neither Ehrlichia/Anaplasma nor Babesia was found in human specimens in the Novosibirsk region.