A new species of the geckonid genus Mediodactylus (thin-toed geckos) was discovered from Qom Province, Iran. Based on a combination of features including small body size (up to 32 mm SVL), a relatively small, triangular mental plate that is pointed posteriorly, and three pairs of postmentals with the first pair broadly contacting each other, the new species can be separated from other Iranian Mediodactylus. Dorsal scales heterogeneous, juxtaposed enlarged strongly keeled tubercles in 10 longitudinal rows; subcaudal scales are small and keeled, with no medial row of transversal enlarged plates. Dorsal patterns consist of six narrow black crossbars between limbs, with wider grayish or brownish interspaces in between, usually two bands on the occipital region and neck, 12–14 dark crossbars on the tail. We found a significant genetic distance (minimum genetic distance: 8.2) between our new species and other species by analyzing the sequencing of a fragment of the first subunit of cytochrome b (Cytb; 629 bp). Phylogenetically, it forms a highly divergent lineage with sister relationships to Mediodactylus aspratilis and Mediodactylus heterocercus. Herein, we provide an identification key and comparisons with other species of Mediodactylus.