Biomass coverage of the Serra do Gerês, Serra Amarela, Serra do Peneda and Serra do Soajo, as well as the Mourela and Castro Laboreiro plateaus, are dominated by four distinct biomes: oak forest, shrubbery, marshes and riparian vegetation.

The floristic diversity includes 823 vascular taxa that occur in 128 types of natural vegetation. The oak forests which are common throughout the park, are specifically concentrated in Ramiscal, Peneda, Gerês and Beredo river valleys. These forested are dominated by an alliance between the Pyrenean (Quercus pyrenaica) and English (Quercus robur) oaks, which themselves are differentiated among the lower altitudes and exposed flanks (the Rusceto-Quercetum roboris) and those oaks with Atlantic characteristics (Myretillo-Quercetum roboris). The first association are commonly found with English oak (Quercus rober), Cork oak (Quercus suber), Butcher’s broom (Ruscus aculeatus), Maple (Acer pseudoplatanus) and Portuguese laurel (Prunus lusitanica), while the second association unites the English and Pyrenean oaks with Bilberry (Vaccinium myrtillus), Strawberry tree (Arbutus unedo) and European holly (Ilex aquifolium). In upper altitudes there are patches of English oak that enter into their own association (Holco-Quercetum pyrenacia), which is integrated into another group (Quericon robri-patraea). These oaks have been, over the course of human settlement, the object of intense use, resulting in a general degradation of the spaces into nothing more than shrubbery.

The bush and shrublands, which characterize the remainder of the spaces (74% of the park), are dominated by dwarf (Ulex minor) and European (Ulex europaeus) gorse andheather (Erica umbellata and Calluna vulgaris), with a mixtures of common juniper (Juniperus communis), southern heather (Erica australis) in the upper altitudes, while lower altitude bush includes cross-leaved heather (Erica tetralix), dwarf gorse (Ulex minor), Dorset heath (Erica ciliaris), common sundew (Drosera rotundifolia), pale butterwort (Pinguicula lusitanica), marsh violet (Viola palustris) and purple moor grass (Molinia caerulea).

Riparian and marshlands along the river courses are also sites of rare species of Chain ferns (Woodwardia radicans), Willow (Salix repens), Downy Birch (Betula pubescens), Deciduous shrubs (Spiraea hypericifolia), Portuguese Enchanter’s nightshade (Circaea lusitanica) and Angelica herbs (Angelica laevis).

There are 627 flora species identified by Serra and Carvalho (1989) as under pressure and considered endangered, which included two medicinal plants: Tutsan (Hypericum androsaemum) and Sundew (Drosera rotundifolia). Based on the protection list of botanical species, and UICN categories: 18 are considered in risk of extinction, 17 are vulnerable and one is rare. They also identified two species as extinct within the park boundaries: a Geranium (Geranium lanuginosum) and Fragrant orchid (Gymnadenia conopsea). There are three endemic species. Those factors that have been identified that threaten these habitats include: natural and manmade fires, use of forest for fuel wood and agricultural use of habitats.