The genus Polianthes (Agavaceae) is endemic to Mexico and is important at the scientific, economical, and cultural level since prehispanic times. Habitat destruction is one of the main factors affecting populations of Polianthes species, yet little is known about the geographic distribution of this genus, and thus its vulnerability to habitat change. We compared three different approaches to measure the Polianthes species area of distribution to assess the risk of species extinction applying the MER (Method of Evaluation of Risk extinction of wild species for Mexico): area of occupancy, extent of occurrence, and ecological modeling. We also found the richness areas of distribution of this genus. We compared the species distributions with Terrestrial Protected Regions (TPR) and Natural Protected Areas (NPA). Although the three methods used to calculate the species area of distribution agree about the highly restricted nature of Polianthes species. The area of occupancy sub-estimate the species distribution, while the extent of occurrence over-estimate it for species with disjoint distribution. Thus, we recommend the use of ecological modeling to improve the assessment of the current species distribution area to apply the MER. Most Polianthes species are distributed in the Sierra Madre Occidental and Transvolcanic Belt. Three species do not occur in any of the NPA or TPR, one species has suitable habitat in three TPR but has not been recorded there, and one species, P. palustris, is likely extinct.