Distributional patterns of 81 species of three genera of Mexican gymnosperms (Ceratozamia, Dioon, Pinus) were analyzed to evaluate their contribution to the cladistic biogeography of the Mexican Transition Zone, applying Brooks Parsimony Analysis (BPA) and parsimony analysis of paralogy‐free subtrees (PAPS). BPA showed three main groups of areas: clade A is comprised of the Baja California, Great Basin, and Mojavean provinces; clade B includes the Valle de Tehuacán‐Cuicatlán, Balsas Basin, Planicie Costera del Noreste, Planicie Costera del Noroeste, Costa del Golfo de México, and Costa Pacífica provinces, located along the coasts and in the central lowlands of Mexico; and clade C includes the Appalachian, Atlantic and Gulf Coastal, Yucatán Peninsula, Caribbean, Californian, Vancouverian, Eastern Central America, Soconusco, Serranías Transístmicas, Serranías Meridionales, Sierra Madre Occidental, Altiplano, and Sierra Madre Oriental provinces, corresponding to the montane areas of the Mexican Transition Zone, Central America and some areas of the U.S.A. PAPS showed three groups of areas: clade D includes the Vancouverian, Appalachian, and Atlantic and Gulf Coastal provinces; clade E the Balsas Basin, Planicie Costera del Noreste, and Planicie Costera del Noroeste provinces; and clade F the Serranías Transístmicas, Soconusco, Serranías Meridionales, Sierra Madre Occidental, Altiplano, Sierra Madre Oriental, Baja California, Californian, Great Basin and Mojavean provinces. Comparing both analyses, three common area relationships emerge: (1) Appalachian and Atlantic and Gulf Coastal provinces, (2) Great Basin, Mojavean and Baja California provinces, and (3) Altiplano, Sierra Madre Oriental and Sierra Madre Occidental provinces. Differences between the general area cladograms can be accounted for by dispersal having a stronger influence in BPA, and the PAPS general area cladogram showing a clearer vicariant signal. The general area cladograms obtained support some area relationships not explained in previous studies, and may complement the historical distributional patterns of the biota of the Mexican Transition Zone.