The Pieniny botanical heritage is rich and varied. The richness of the vegetation has been influenced by many factors including the underlying calcareous limestone, exceptionally varied geomorphology and microclimatic conditions, a lack of glaciations, the proximity of the Tatra Mountains and also the prevalent conditions which favour natural dispersal of flora between the ranges.

Many natural communities co-exist in Pieniny; visitors can find afforested areas as well as rock and scree clusters. There are also semi-natural communities (meadows and pastures) which have resulted from human land-use. So far about 1,100 species of vascular plants, 280 species of algae, 290 species of mosses (Bryopsida) and liverworts (Hepaticopsida), 435 species of lichen (Lichenes), 558 species of parasitic fungi and 698 species of large fruit-bodied fungi have been documented.

It is worth mentioning that some endemic species exist in Pieniny (meaning that they occur nowhere else in the world): Pieniny Dandelion Taraxacum pieninicum,  Pieniny Treacle-mustard Erysimum pieninicum, and also 3 endemic varieties: the Pieniny type of Cornflower Centaurea triumfettii var. pieninica, and the calcareous types of Biting Stonecrop Sedum acre var. calcigena and Wormwood Artemisia absinthium var. calcigena.
Relicts can also be found in this area, i.e. species preserved since earlier geological periods in refugia cut off from the main population of their more common relatives. These are quite distinctive when compared with the usual population of a given species e.g. Zawadzki Ox-eye Daisy Dendranthema zawadzkii, Savin Juniper Juniperus sabina and Mountain Avens Dryas octopetala.

Three basic environment complexes which differ markedly in type of plant cover are classified in the Pieniny area:
* Dunajec valley with its larger tributaries (Krośnica and Grajcarek). This complex is characterised by lack of natural plant communities over large parts of the area - mostly lack of marshy meadows (large parts of lower-lying areas are dominated by human settlements, ploughed fields, meadows and pastures).
* Northern slopes, dominated by mesophilous beech-fir forests, ploughed fields and meadows.
* Strongly sunlit southern slopes, where natural epilithic communities and xerothermic fir and beech stands are found. Farmland and dry pastures also occupy these slopes.