Mexico is home to the highest species diversity of pines: 46 species out of 113 reported around the world. Within the great diversity of pines in Mexico, Pinus culminicola Andresen et Beaman, P. jaliscana Perez de la Rosa, P. maximartinenzii Rzed., P. nelsonii Shaw, P. pinceana Gordon, and P. rzedowskii Madrigal et M. Caball. are six catalogued as threatened or endangered due to their restricted distribution and low population density. Therefore, they are of special interest for forest conservation purposes. In this paper, we aim to provide up-to-date information on the spatial distribution of these six pine species according to different historical registers coming from different herbaria distributed around the country by using spatial modeling. Therefore, we recovered historical observations of the natural distribution of each species and modelled suitable areas of distribution according to environmental requirements. Finally, we evaluated the distributions by contrasting changes of vegetation in the period 1991–2016. The results highlight areas of distribution for each pine species in the northeast, west, and central parts of Mexico. The results of this study are intended to be the basis of in situ and ex situ conservation strategies for the endangered Mexican pines.