One Rickettsia sp. (OTU 83718) accounted for 89% of all Rickettsia OTUs and matched 99–100% to R. rhipicephali (GenBank accession numbers CP013133.1, NR_074473.1, CP003342.1, NR_025921.1, and U11019.1). It also had 99% identity to other Rickettsia; however, E values were 100× higher to these other Rickettsia sequences. The second most abundant OTU (553807) accounted for 0.7% of all Rickettsia OTUs and was 99% identical to several different R. rickettsii strains including R. philipii str. 364D (GenBank: NR_074470.1) as well as other strains of R. rickettsii (including GenBank accession numbers CP006010.1, NR_102941.1, and CP003311.1). All other Rickettsia OTUs comprised less than 0.09% of total Rickettsia OTUs. OTU 840032 comprised 87.4% of all Francisella OTUs and matched 100% with Francisella-like endosymbiont (FLE) of D. occidentalis (GenBank accession numbers AY805304.1, and AY375402.1). The next closest matches were Francisella endosymbionts of other tick species D. albipictus, D. andersoni and D. variabilis (GenBank accession numbers GU968868.1, FJ468434.1, and AY805307.1, respectively). The next most abundant Francisella OTU (399541) (GenBank acc. KU355875.1, this paper) accounted for 3.1% of all Francisella OTUs and matched 97% with gene sequences of endosymbionts previously determined from a spectrum of Dermacentor species including Dermacentor occidentalis (AY375403.1), D. albipictus (GU968868.1), D. variabilis (AY805307.1), D. nitens (AY375401.1) and D. andersoni (AY375398.1). All other Francisella OTUs accounted for less than 0.4% of the total Francisella OTUs.