The Protected Area's flora is characterised not only by the wide range of plant species, but also by the presence of many endemic species and sub-species, 97 of them endemic to Crete and 15 steno-endemic to smaller areas. There are no precise numbers for the plant species found in the Samaria National Park, but there is an ongoing extended floristic monitoring program covering 15 out of the 19 identified habitats of the Protected Area, which includes all the steno-endemic and protected species found in the Area.

19 different types of habitats have been identified and mapped over the extent of the Samaria National Park area. The habitats identified, according to Natura 2000 classification, are: 1120-Posidonia beds (Posidonion oceanicae), 1240-Vegetated sea cliffs of the Mediterraneancoasts with endemic Limonium spp., 1310-Salicornia and other annuals colonising mud and sand, 2230-Malcolmietalia dune grasslands, 3170-*Mediterranean temporary ponds, 4090-Endemic oro-Mediterranean heaths with gorse, 5420-Sarcopoterium spinosum phryganas, 5430-Endemic phryganas of the Euphorbio-Verbascion, 6220-*Pseudo-steppe with grasses and annuals of the Thero-Brachypodietea, 8140-Eastern Mediterranean screes, 8210-Calcareous rocky slopes with chasmophytic vegetation, 8310-Caves not open to the public, 8320-Fields of lava and natural excavations, 9290-Cupressus forests (Acero-Cupression), 9320-Olea and Ceratonia forests, 9540-Mediterranean pine forests with endemic Mesogean pines, 92C0-Platanus orientalis and Liquidambar orientalis woods (Plantanion orientalis), 92D0-Southern riparian galleries and thickets (NerioTamaricetea and Securinegion tinctoriae) and 934A-Greek Quercus coccifera forests. Of these types, some are considered already in a critical state, while others are well established and thriving. Furthermore, the classification takes into account the habitats' spread pattern in order to assess their conservation priority level. Thus, three classes of priority have been established, with 5 out of 16 habitats' identified ranking in the highest class of importance.