Land management and biodiversity protection are highly dependent on ecosystem classification. To identify the ecosystems, often ecologically homogenous areas are distinguished based on physical and biological features at various scales. These areas can also be considered as biodiversity surrogates for protection policies and planning. We classified the terrestrial areas of Iran into ecosystems using revised and updated layers of landform and climate as our two main criteria. Moreover, we applied a revised vegetation layer as the confirmatory criterion. At a scale of 1:1,000,000, we obtained a total of 119 homogenous ecological units, and based on the dominant vegetation types, we classified them into 21 terrestrial ecosystems at the national level. Of these ecosystems, 11 were dominated by vegetation, and the remaining 10 had sparse nondominant vegetation. Evaluation of the least and most frequent ecosystem patches and ranking of their size classes using landscape metrics provided an information basis for better land protection planning. We maintain that each ecosystem needs to be represented by a protected area and its size and distribution also helps us form a comprehensive and effective protection network in Iran.