A species with populations that occur in variety of habitats might be expected to exhibit variation in morphological traits across its distribution. Based on our examination of 95 specimens of Bunopus tuberculatus (Squamata: Gekkonidae) collected across its range within Iran, we describe the geographic variation in meristic traits and morphology. Values for traits were compared using principal component analysis and discriminant function analysis. None of the populations showed sexual dimorphism in morphometric or meristic characters. One-way analyses of variance revealed that differences exist in most characters among populations. Additionally, canonical variable analyses indicate that the sampled populations of B. tuberculatus are divided into four distinct forms: (1) western and southwestern populations, (2) southern populations, (3) the population of Bampoor, and (4) eastern populations. Our results provide a comparative baseline that will help to resolve the complicated taxonomy of B. tuberculatus across the rest of its distribution in southwest Asia and the Arabian Peninsula.