The chinkara (Gazella bennettii, Sykes 1831) exhibits a broad distribution from Iran to India and has been categorized into five species: G. bennettii, G. christyi, and G. salinarum representing the Indian chinkara, and G. fuscifrons and G. shikarii pertaining to the Iranian chinkara (jebeer). This classification within the "Gazelle bennettii group" is solely based on morphological data, lacking genetic information. To investigate the potential presence of multiple species within the group and to determine subspecific variations, we sampled jebeer in Iran and conducted phylogenetic analyses using cytochrome b, COI, and sequences from two nuclear introns (CHD2 and ZNF618). Our mitochondrial data revealed a significant divergence within the "Gazelle bennettii group," identifying two lineages: the Iranian lineage (jebeer) and the Indian lineage (chinkara). Estimates of divergence time suggest that the split between jebeer and chinkara occurred approximately 0.895 million years ago, possibly associated with a vicariant event caused by the Indus River. These findings have important implications for assessing species conservation statuses on the IUCN Red List because an endangered lineage (jebeer) is currently grouped together with a non-threatened one (chinkara) under the same global assessment, which underestimates the true endangered status of jebeer. In Iran, the haplotype distribution map of the jebeer can serve as a fundamental genetic framework guiding conservation efforts across Iranian protected areas and captive breeding centers. Therefore, we recommend any future management plan should be based on these findings and treat these two lineages separately.