The territory of the museum-preserve includes pine forests rare for the Kemerovo region which extend along the right bank of the Tom in a narrow strip, and small areas of meadows and birch forests too. Along the river Pisanaya one can see brushwoods of flood plain willow beds. Stony southern slopes of the native bank of the Tom are covered with steppe plants. The flora of the "Tomskaya Pisanitsa" is abundant and varied. On the territory of the museum there are about 400 species of higher plants (these are about of the whole flora of the Kemerovo region); among them — 39 species of trees and bushes, the rest are herbaceous plants. About 40 species of the plants are rare for Kuzbass and need protection, 5 species are tertiary relics, 1 species — Stipa pennata — is included into the Red Book.

A pine forest occupies about 90% of the preserve territory. Along the river Pisanaya one can see brushwoods of flood plain willow beds. Stony southern slopes of the native bank of the Tom are covered with steppe plants. Here one can meet such plants as Pteridium aquilinum, Aegopodium podagraria, Carex macroura, Lilium martagon, Adenophora liliifolia, Pyrda media – dozens of species of meadow herbs. Steppe vegetation includes such plants rare for the region as Dianthus versicolor, Viola rupestris, Allium nutans, Festuca valessiaca, Stipa capillata, Thymus serpyllium.