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We discovered a previously unrecognized evolutionary lineage of Eremias assigned to the subgenus Rhabderemias in the Pakistan–Afghanistan border region. Although superficially similar to the recently described Iranian species E. graphica in its vermiculate dorsal pattern, mitochondrial phylogenetic analyses recover this lineage as sister to E. fasciata, while nuclear DNA data independently support its distinctiveness. The new lineage was recorded from low, mobile sand dunes in northwestern Balochistan, Pakistan, at the southeastern margin of the Registan Desert. It is clearly differentiated from E. fasciata by both mitochondrial and nuclear markers, with mean uncorrected p-distances of approximately 10.6% for mitochondrial DNA and 0.9% for nuclear DNA. Morphologically, it differs from most species traditionally assigned to Rhabderemias in retaining a vermiculate dorsal pattern in both juveniles and adults rather than the longitudinally striped pattern characteristic of the group. It is further distinguished from E. graphica and the sympatric E. fasciata by a combination of dorsal coloration, scalation, body proportions, and habitat association, with multivariate morphological analyses supporting its distinctiveness from both species. Given the continuity of suitable sandy habitats across international borders, the new species is likely to occur more widely within the Registan Desert of southwestern Afghanistan and possibly adjacent eastern Iran. Our integrative analyses also provide the first definitive confirmation of the long-debated occurrence of E. fasciata in Pakistan. These findings increase the known diversity of Rhabderemias to 12 species, five of which occur in Pakistan, and bring the total number of Eremias species recorded from the country to eight.