Magnolia vovidesii has been found in a few small patches in central Veracruz, Mexico. Previous ecological studies have suggested high reproductive potential and stable population growth; however, in the last 20 years, there have been severe anthropogenic environmental impacts on the species. The main objectives of this study were (a) to document the current trend of the population, (b) to determine its spatial structure, and (c) to identify the main threats to the species in order to propose conservation and management strategies. Our results show a population in decline, caused by high mortality during early establishment stages (seeds and seedlings) and the removal of young sick trees during the reproductive stage. We found a strong spatial dependence between seedlings and reproductive individuals (young and old adults) and a weak spatial association between reproductive stages, suggesting a nursing effect, inbreeding, and pollen dependence. The main threats to the population are frequent plant removal, trails used by people, land-use change, and parasitism. These data show the urgent need to carry out prompt conservation action for the species, with special emphasis on ex situ propagation. The results of this study suggest that M. vovidesii should be transferred to the International Union for Conservation of Nature Red List category for critically endangered species.