Amphibians are severely threatened and declining globally. Although more than 40 percent of amphibians are already at risk of extinction, they have remained the world's least represented within protected area networks. Amphibians represent the highest number of (sub-) endemics of vertebrates in Iran. In this study, we assessed the representation of amphibians in the current network of protected areas in Iran, identified the hotspots for amphibian species, and then prioritized areas for the effective conservation of amphibians at the national level. We curated 2242 observation points for the 22 amphibians, including 16 species of Anura and 6 species of Caudata, based on extensive literature review and frequent attempts for validation of the uncertain reports and sampling where needed. We used these occurrence points along with bioclimatic variables to train species distribution models for amphibians at spatial resolution of 30 arc second in Iran. We evaluated the performance of our distribution models using the discrimination capacity as well as goodness-of-fit. We excluded the two species, Firouzophrynus stomaticus and Neuregus crocatus, from our analysis since the quality of their models were not satisfactory. We prepared the national diversity and range-rarity maps and calculated the hotspots for amphibians in Iran based on the top 10% of areas with highest diversity and range-rarity score. Our results show that despite the national conservation efforts to expand the protected area network, the identified priority areas for amphibians are inadequately represented in the current protected area network. We identified two main key regions for amphibian conservation namely, the Caspian Hyrcanian Mixed Forest, and Zagros Mountains forest steppe which is already part of the Irano-Anatolian global biodiversity hotspot. We believe our outcome provides scientific evidence on the priorities for conservation of amphibians and thus the expansion protected area network.