The genus Microgecko Nikolsky includes eight species distributed across Iran, Pakistan, and northwestern India. In this study, we describe a new species of Microgecko based on molecular and morphological data. Four specimens were collected from a remote plain surrounded by mountains in southern Iran. The new species, Microgecko khabrensis sp. nov. is distinguished from its congeners by a combination of morphological features, including distinct coloration (dark blotches on the flanks and sacrum, lower number of caudal crossbars) and unique scalation patterns (a combination of greater number of scales on head, number of postmentals, number of scales bordering the nostril, number of upper and lower labials). Molecular analysis based on a 601 bp fragment of mitochondrial gene Cytb revealed that M. khabrensis sp. nov. is a distinct evolutionarily significant unit (ESU) within the genus Microgecko. M. khabrensis sp. nov. is the closest relative to M. chabaharensis, among other congeners, based on both morphological and molecular evidence. A literature-based morphological comparison of M. khabrensis sp. nov. with other species of the genus and an updated key for Microgecko spp. are presented.