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As a vector of wide range of pathogenic agents, ticks pose health threats to wild and domestic animals, and humans. Information is unavailable about the prevalence and spatial survey of <i>Hyalomma kumari</i> ticks and associated <i>Rickettsia</i> spp. in Pakistan. Concerning this knowledge gap, the present study aimed to molecularly detect <i>Rickettsia</i> species associated with <i>H. kumari</i> infesting small ruminants in Khyber Pakhtunkhwa (KP), Pakistan. A total of 409 <i>H. kumari</i> ticks were collected from 163/295 infested hosts with an infestation rate of 55.25%. A total of 204 females, 158 males, and 47 nymphs were collected. Goats were heavily infested by 224 ticks having an infestation rate of 58.33% (98/168), whereas sheep were infested by 185 ticks having a lesser infestation rate of 51.18% (65/127). Genomic DNA extracted from ticks was used for the amplification of tick (<i>cox I</i>, 16S rRNA, ITS-2) species and <i>Rickettsia</i> (<i>gltA</i>, <i>ompA</i>, and <i>ompB</i>) partial genes. Eighty-three ticks were subjected to PCR, and 8/83 (9.6%) were found positive for rickettsial agents. The <i>cox I</i> and 16S rRNA sequences of <i>H. kumari</i> showed 98.90–99.74% identity with <i>H. kumari</i> sequences reported from Pakistan, and phylogenetically clustered to the corresponding species reported from Pakistan and India. The obtained rickettsial <i>gltA</i>, <i>ompA</i>, and <i>ompB</i> sequences showed 100% identity with <i>Rickettsia</i> sp. of the <i>Rickettsia conorii</i> reported from Pakistan. In the phylogenetic trees, rickettsial sequences clustered with uncharacterized <i>Rickettsia</i> sp. from Pakistan and <i>R. conorii</i> from Israel, Russia, South Africa, and India. The present molecular based detection of <i>H. kumari</i>-associated <i>R. conorii</i> will facilitate effective surveillance in the region.