The Malinalco-Tenancingo-Zumpahuacán Protected Natural Area measures roughly 150 km², within the eponymous municipalities in the State of Mexico. We undertook a comprehensive flora of the region to obtain a database with 7,187 records. The identified specimens comprise 165 families, 724 genera, and 1,704 species. The most representative families are Asteraceae with 85 genera and 191 species; Leguminosae with 51 genera and 136 species (Fabaceae 79, Mimosaceae 43 and Caesalpiniaceae 14); Poaceae with 40 genera and 89 species; and Orchidaceae with 40 genera and 90 species. We identified six distinct types of vegetation: tropical deciduous forest, tropical subdeciduous forest, montane mesophytic forest, Quercus forest, Pinus-Quercus forest, and gallery forest. In addition, we provide a list of 287 endemic species and 336 new species reports for the State of Mexico.