Cape Breton Highlands National Park has 78 rare vascular plants, including boreal and arctic-alpine disjuncts (plants that are separated from the rest of their range in North America) and northeast North American endemics (plants that are found only in the northeastern states and Canada).

The rare plants are located in specific habitats found in the park. Some species are found in habitats with unstable substrates, low air temperatures and high humidity which is favourable to cold-adapted plant species. Boreal and arctic-alpine disjunct species are plants that were widespread immediately following the last ice age but are now limited in their range. As the climate became warmer these plants survived only in favourable locations, such as cool areas or headlands along the coast, the plateau, and deep ravines or shaded cliffs.

The park also harbours 29 rare moss and liverwort species.