Sitia Natural Park presents great floral interest. Amongst the hundreds of plant species it hosts, there are many endemic species encountered throughout Crete, endemic to Crete and Kasos, as well as unique species, known only to the southeast Aegean. The region as a whole belongs to the Mediterranean Vegetation Zone, where brush vegetation prevails. Variations in the vegetation are small, with some exceptions in areas such as the Vai Palm Forest and the surrounding area, as well as in some canyons with an intense presence of water, at least during winter months (Zakros canyon, Xerokambos, Chochlakia). The existence of great expanses of olive trees, vineyards and other tree crops is also very important for the composition of the island’s flora.

The brush that covers many parts of the park, both coastally and in the mountain area, are dominated by low, thorny and spherical bushes, such as the Thorny Burnet (Sarcopoterium spinosum), Thyme (Coridothymus capitatus), Broom (Genista acanthoclada), Winter Savuory (Satureja thymbra) and Greek Spiny Spurge (Euphorbia acanthothamnos). They coexist with non-thorny bushes such as Heather (Erica manipuliflora), Ballota acetabulosa, Greek Sage (Salvia fruticosa) and the Rock Rose (Cistus creticus, Cistus salviifolius). On smaller expanses of land, taller bushes are encountered, forming maquis vegetation and consisting of Mastic (Pistacia lentiscus), Spiny Broom (Calicotome villosa), Wild Olives (Olea europaea subsp. Oleaster), Phoenician Juniper (Juniperus phoenicea), Kermes Oak (Quercus coccifera), Carob trees (Ceratonia siliqua), Osyris alba, oleander (Phlomis fruticosa) and Tree Spurge (Euphorbia dendroides). Other plants that grow in the ravines in the area of Zakros, where there is plenty of water, are Oriental Planes (Platanus orientalis), Oleander (Nerium oleander) and Vitex (Vitex agnus castus).
The region’s canyons offer refuge to many important species of flora in the area. The canyons of Kato Zakros and Chochlakia, in particular, are home to a large number of plants and they attract many researchers and observers every year. Characteristic species that have found a home on the sheer limestone rocks and on the ravine beds are Αristolochia cretica, Delphinium staphisagria, Wild Carnations (Dianthus juniperinus), Εuphorbia dendroides, the Lecokia cretica, Εphedra cambylopoda, Nepeta melissifolia , Capers (Capparis spinosa), the Dracunculus vulgaris, bluebells (Campanula pelviformis and Campanula spatulata ssp. Filicaulis), Jerusalem Sage (Phlomis lanata), Oregano (Origanum onites), Tulipa saxatilis and many orchid species.

Coastal areas are dominated exclusively by herbaceous plants, mainly Amaranth (Limonium greacum) and the endemic Limonium sitiacum, while on the beaches of Katsounaki and Argilos in Xerokambos, there are Sea Daffodil (Pancratium maritimum).