The flora of Mashpi is defined by its geography. With its steep gradient, the higher zone is dominated by relatively short trees. It is densely inhabited by aerial plants like bromeliads, orchids and moss, which take advantage of this location to feed on the delicacies carried in by the clouds. Ferns and lobster claws rise up from the ground, and as well as various relations of coffee (Rubiaceae), with sweet-scented and striking flowers.

Much of the reserve has been affected by wood extraction over a long period of time and is still in the process of recovery. In these areas the most representative trees are pioneers like the Guarumo that grow quickly in the places where other trees have fallen, preparing the ground so that it can then be occupied by larger, longer-living trees. Even so, the reserve maintains parts intact where a high level of endemism is evident.

In total 179 species of plants belonging to 61 families have been registered, and there is still much to explore and discover. In the year 2014 a new species of magnolia was identified in the reserve, the Mashpi Magnolia, which is endemic to the reserve. It is a tall tree with distinctive large, white flowers and can easily be observed from “La Libélula”, in the highlands of Mashpi.