The area of ​​the National Park presents a rich and diverse flora with species typically met in the Eu-Mediterranean and Para-Mediterranean vegetation zones. The composition of the forest, that covers the greatest part of the National Park, has been shaped in accordance to the climatic conditions in the area, geomorphology, soil and proximity to the Evros River. The vegetation is mainly composed by black pine (Pinus nigra) and Turkish pine (Pinus brutia) mixed with oaks (Quercus spp.) and other deciduous species, as well as maquis shrublands.

At the central and eastern part of the National Park we find coniferous forests, dominated by Turkish pines (Pinus brutia) and secondarily by Black pines (Pinus nigra), while deciduous forests, mixed forests and maquis vegetation only cover small areas. On the contrary, in the north and south-west, pure oak forests dominate, composed by several oak species such as the Broadleaved oak (Quercus frainetto), the Turkey oak (Q. cerris) and the Downy oak (Q. pubescens), which have suffered intense logging in the past. In the intermediate zones, mixed forests of oaks and pines have been formed. Sclerophyllous shrubs, such as the Greek Strawberry tree (Arbutus adrachne), the Phillyrea (Phillyrea latifolia), the Treeheath (Erica arborea) and the Cretan rockrose (Cistus creticus) are mainly found in the south-western area.

Regarding riparian vegetation, the common Black alder (Alnus glutinosa) dominates most sites, while in others the Willow (Salix spp.), the Black poplar (Populus nigra) and the Athel (Tamarix spp.) stand out.

Up to today, 360-400 plant species have been recorded in the National Park. Among them we find two species endemic to Greece (Minuartia greuteriana and Onosma kittanae), as well as three rare species (Cephalanthera epipactoides, Salix xanthicolakai Zygophyllum album). Twenty nine plant species are under protection, while remarkable is the presence of 25 orchid species, as well as that of Eriolobus trilobatus, a rare Wild apple tree species with a very narrow distribution.