We focus on lichens and biological soil crusts (BSCs) as representatives of the vast array of cryptogams that participate in ecological communities to varying degrees but are usually under-considered in ecological restorations. Successful rehabilitation of lichens and BSCs will likely require correct diagnosis and amelioration of factors limiting natural recovery such as unstable substrates and/or inadequate microhabitat availability, resource limitations, and propagule scarcity. Lichens contribute notably to biological diversity in many communities and are significant functional components in a subset of those communities (though not of most wetlands and mesic prairies, frequent targets of restoration research). In restoration of wooded communities, retention and/or acceleration of the development of substrate and microhabitat diversity (perhaps in later stages of restoration) are important plan elements for enhancing epiphytic lichen diversity. In more open communities (lichen woodland, tundra, etc.) where ground lichens are functionally important, they should be included in early stages of restoration. BSCs (including lichens, mosses, fungi, algae, cyanobacteria) are critical structural and functional components of many ecological systems characterized by high abiotic stress and discontinuous coverage of ground by vascular plants. In arid land systems, BSCs additionally act as ecosystem engineers by stabilizing the soil surface. Recent studies suggest that rehabilitation of BSCs in highly degraded systems may trigger a transition in the ecosystem to a more highly functional state. We propose that incorporation of lichens and BSCs into ecological restoration should occur early where they are important functionally, and at appropriate stages where they are important as biodiversity reservoirs.