The effects of climate change on biodiversity are imminent, and these turn out to be particularly alarming for the tropical montane cloud forest. The disappearance of fragments of this forest is expected, along with some of their most characteristic species, such as Magnolia schiedeana . Mexico, through the National System of Protected Natural Areas, must consider protection strategies for those species distributed within the Protected Natural Areas that will be affected by the climate change. This study delimits the distribution of M. schiedeana in Mexico, through ecological niche and future distribution modeling under two periods: years 2040 and 2080. These distribution models tend to move towards northeastern Mexico. The potential distribution of this species declines by 0.36% and 1.94% in the first and second periods, respectively. From this result, the future role of National System of Protected Natural Areas in the long-term conservation of M. schiedeana was analyzed, prompting a proposal to focus conservation efforts on the following Protected Natural Areas: (1) At the federal level: Biosphere Reserve Sierra Gorda and Cañón de Metztitlán, Cuenca del Río Necaxa and El Potosí, National Park El Chico, Cofre de Perote, Pico de Orizaba and Los Mármoles, and Nevado de Toluca. (2) At the state level: Cerro de las Culebras, Cerro de la Galaxia, Cerro de Macuiltepetl, El Tejar Garnica, Francisco Javier Clavijero, La Martinica, Molino de San Roque, Pacho Nuevo and Predio Barragán.