In order to optimize conservation policies for endangered plant species in North Africa and minimize the investment of the public resources we explore the capacity of a mountain plant species to persist locally in restricted natural areas. Palaeoecological studies have shown that plant species survived major global climate changes within refugia which offered suitable condition for their long term persistence. Our study aims at identifying potential mountains areas which may play the role of modern microrefugia for preserving locally endangered plant species. We analysed the mountain ruggedness of an area in the North-East of the Middle Atlas mountains where a population of an endangered plant species, Cedrus atlantica, is isolated today around lake Tameda. In addition, we collected a sediment core in the lake to investigate the recent history of the species with the local environmental changes. We compared the terrain and fossil analyses with an area in the Rif mountains where the terrain rugosity is lighter than in the Middle Atlas and where Atlas cedar populations occur as well. Our results show that the Atlas cedar is better preserved in terrains with high rugosity because they offer a wider panel of suitable microclimates for the species persistence and they restrict the number of inhabitants as well which, de facto, reduces the anthropogenic disturbances. We have carried out this analysis at a very small scale (less than 40km2). A more exhaustive analysis of the terrain rugosity over the Atlas and Rif mountains, combined with historical data, will help to identify more suitable refugial areas for preserving the species at a larger scale. Protecting these refugial areas over decades from any anthropogenic activity should be possible at a minimal cost and would represent an immediate response to the ongoing climate change for preserving endangered species.