Borrelia hermsii is a non-Lyme borreliosis pathogen that is responsible for causing tick-borne relapsing fever in humans and animals in the western United States. B. hermsii has been described to encompass two divergent genomic groups， GGI and GGII， which have been suggested to maintain a unique geographical distribution and potential range of pathogenicity. Though the genomic groups have been extensively documented in the literature， a real-time PCR tool for identifying these genomic groups is lacking. This study describes the development and validation of two flaB-based quantitative real-time PCR assays for differentiating between the two genomic groups of B. hermsii while also maintaining specificity against other closely related Borrelia species. The diagnostic specificity of the assays were evaluated using a large panel of various Borrelia species， including a collection of 22 B. hermsii culture isolates purified from various hosts. The high sensitivity and specificity of the assays provide a useful tool for supporting future studies aimed at evaluating the geographical distribution as well as potential intraspecies pathogenicity within arthropod vectors and mammalian hosts.