From the botanical point of view the whole PLA territory belongs to the independent phytogeographical district of Český kras. The vegetation composition here has always been influenced by the variety of geological bedrock (predominantly limestone). Other factors influencing the vegetation composition are the specific geomorphology of the landscape, neighbouring warmer and drier regions, the xerothermic vegetation communities, as well as human influence and settlement. The river phenomenon of the Berounka river and its larger tributaries increases the variety of habitat types and enhances the effects of the karst phenomenon.
A characteristic feature of the area is the occurrence of thermophilous and xerophilous sub-Mediterranean plant species alongside the typical forest flora of central Europe. Some species are on the border of their range here in Český kras, for example, the broom Chamaecytisus ratisbonensis and shrubby milkwort (Polygaloides chamaebuxus). Other species found here are rare or endangered, either in the Czech Republic or throughout Europe, including pyramidal orchid (Anacamptis pyramidalis), Austrian dragonhead (Dracocephalum austriacum), yellow pheasant’s eye (Adonis vernalis), the wallflower Erysimum crepidifolium, the feather grass Stipa tirsa and purple viper’s grass (Scorzonera purpurea). An endemic species in Český kras, the karst variety of rowan (Sorbus eximia) grows in the pannonian downy oak forests and on the rocky steppe.
Český kras is the only larger limestone territory in the Bohemian basin on which communities of heliophilous and xerophilous plants have developed in a complete ecological series from rocky vegetation to dry grassland to forest.
The vegetation of the rocky steppe and rocks is found on two extreme locality types. Steep, south-facing rock walls harbour a number of notable and mostly endangered species such as Bohemian small pasque flower (Pulsatilla pratensis subsp. bohemica), table iris (Iris aphylla), the cornflower Cyanus triumfettii, golden alyssum (Aurinia saxatilis), hoary rock rose (Helianthemum canum), Austrian dragonhead (Dracocephalum austriacum), St. Bernard’s lily (Anthericum liliago), blue lettuce (Lactuca perennis) and others. Damp and shaded limestone walls and cliffs provide shelter for species whose optimal habitat is in the European mountains. Characteristic of this community are blue moor-grass (Sesleria caerulea), live-long saxifrage (Saxifraga paniculata), Irish saxifrage (S. rosacea), buckler mustard (Biscutella laevigata) and cheddar pink (Dianthus gratianopolitanus).
The transition between grassland and forest vegetation is formed by the downy oak forests with cornelian cherry (Lathyro versicoloris–Quercetum pubescentis community). They form low-density stands of mostly dwarf growths on the very shallow soils on the limestone rocks. Besides downy or pubescent oak (Quercus pubescens) a range of bushes and shrubs also grow here, including common whitebeam (Sorbus aria), wild service tree (Sorbus torminalis), cornelian cherry (Cornus mas), dogwood (Cornus sanguinea), common privet (Ligustrum vulgare), common barberry (Berberis vulgaris), common buckthorn (Rhamnus cathartica) and others. Notable species which occur in the herb layer include burning bush (Dictamnus albus), snowdrop windflower (Anemone sylvestris), the vetchling Lathyrus pannonicus, purple gromwell (Lithospermum purpurocaeruleum) or lady orchid Orchis purpurea).
Neighbouring the white or pubescent oak forests, on areas with decalcified soil, we can find cinquefoil oak forests Potentillo albae–Quercetum with acidophilous species such as sheep’s fescue (Festuca ovina) and a range of species which indicate the impermeable clay soil such as white cinquefoil (Potentilla alba), sawwort (Serratula tinctoria), betony (Betonica officinalis) or northern bedstraw (Galium boreale).
The most widespread forest community is oak–hornbeam forest Melampyro nemorosi – Carpinetum association with many rare plant species such as martagon lily (Lilium martagon), bastard balm (Melittis melissophyllum), mezereon (Daphne mezereum), and members of the orchid family including narrow-leaved helleborine (Cephalanthera longifolia), elder–flowered orchid (Dactylorhiza sambucina) and lesser butterfly orchid (Platanthera bifolia). A small population of lady bells (Adenophora liliifolia) can be found in the Karlštejn reserve and in the Karlické údolí.
The remnants of the calcicolous beech forests – Cephalanthero-Fagenion cover a much smaller surface area, with the characteristic occurrence of red helleborine (Cephalanthera rubra). This is the lowest elevation in Central Bohemia where European beech (Fagus sylvatica) can be found growing naturally.
On the steep slopes covered with rough talus and boulders, tree species such as Norway maple (Acer platanoides), sycamore (Acer pseudoplatanus), broad–leaved lime (Tilia platyphyllos) and scattered beech grow. In the undergrowth we can find hazel (Corylus avellana), European elder (Sambucus nigra), wild gooseberry (Ribes uva-crispa) and mountain currant (R. alpinum). The spring flowering species in the herb layer include bulbous fumewort (Corydalis cava) and the fumewort Corydalis intermedia, hepatica (Hepatica nobilis), the lesser celandine (Ficaria verna subsp. bulbifera), nine-leaved toothwort (Dentaria enneaphyllos), yellow dead nettle (Galeobdolon luteum) and occasionally with Alpine wolfsbane (Aconitum lycoctonum).
With regard to the permeable bedrock and soil, wetland plant communities are not well developed in Český kras. The banks of the Berounka river are lined with riverbank communities with reed canary-grass (Phalaris arundinacea) and willows (Salix spp.). In some of the wider stream valleys marsh marigold (Caltha palustris) and oat–grass meadows have developed after regular hay cutting.
The limestone bedrock and the variety of habitat types allow the occurrence of more than 330 species of mosses, of which nearly a quarter are endangered species. Sub–Mediterranean species are often found on the sunny rocks and steppes, including Mannia fragrans or Crossidium squamiferum. On shaded rocks and talus fields, endangered species such as Pedinophyllum interruptum or Porella arboris-vitae can be found. An interesting phenomenon is the Tuffa cascades on streams in the karst ravines, where the mosses are a living factor in their formation. Here we can find Palustriella commutata and Pellia endeviifolia.
Český kras is also notable for the occurrence of many xerophilous and thermophilous fungii species. Early in spring we can find the eye-catching scarlet elfcup (Sarcoscypha austriaca), in May and June the morel fungus (Verpa bohemica) and the endangered devil’s bolete (Boletus satanus) can occasionally be found in the oak–hornbeam forests. Much rarer fungi are the truffle Tuber aestivum or the fungus Caesar’s amanita (Amanita caesarea). A wide variety of rotting fungi grow in the damp talus forests and in the beechwoods.