Two previously undescribed rickettsiae were detected in Ixodes ricinus Ricketts by polymerase chain reaction. Ixodes ricinus Slovakia (IRS)3 and IRS4 were identified in ticks collected in northeastern and southwestern Slovakia, respectively. Sequences of the 16S rRNA citrate synthase (gltA) and outer membrane protein rOmpA (ompA) encoding genes of both strains were nearly identical but were distinct from those of all other known rickettsiae. Phylogenetic relationships inferred from the comparison of these sequences with those of other members of the genus Rickettsia indicate that IRS3 and IRS4 constitute a new rickettsial genotype and form a separate cluster among the spotted fever group rickettsiae.