We describe and illustrate Magnolia mixteca, a new species of Magnolia sect. Macrophylla from the Alto Balsas Basin in Oaxaca, Mexico, providing information about its ecology, biogeography and conservation status. Magnolia mixteca differs from M. nuevoleonensis in having larger flowers, longer petals, a yellow petal-blotch, a tan-sand coloured ovary and more numerous stamens and carpels. In addition, we provide a distribution map and key to species of sect. Macrophylla. The relict distribution of this species allows us to consider it endangered (E).