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Approximately 55% of the park is characterized by the Waterberg Moist Bushveld vegetation type (veld type 12).

This vegetation type occurs in the intermediate to high lying areas in the southern and south-eastern portions of the park. This area is characterized by relatively high rainfall (719 mm) and the resultant leaching of the soils results in a fairy low soil nutrient status. This limiting factor in turn results in a fairly low carrying capacity and only ubiquitous species such as kudu and common reedbuck are common in these areas. This vegetation type is characterized by Transvaal beechwoods (Faurea salinga), proteas (Protea caffra) and stem fruit trees (Englerophytum magaliesmontanum). The vegetation along the tarred road leading to the towers are typical of the vegetation type.

Another major vegetation type is the Mixed Bushveld (veld type 18), which covers approximately 42% of the park. This vegetation type is mainly found in the northwestern and isolated southwestern pockets of the park. It occurs predominantly on the undulating to flat plains and the soils are generally clayey, deeper and more nutrient-rich. Most of the charismatic game species such as black rhino, elephant and wild dog will be associated with this vegetation type. This vegetation type is characterized by species such as silver cluster leaf (Terminalia sericea), sickle bush (Dichrostachys cinerea) and round-leaved teak (Pterocarpus rotundifolias). The vegetation around the camping site and tented camp is typical of this vegetation type.

Less than 3% of the park is comprised of Sweet Bushveld (veld type 17). This veld type is mostly found along the banks of the Matlabas River and forms an important winter refuge area for game particularly during limiting periods at the end of the dry season. The planned western expansion of the park will include more of this vegetation type, which is crucial to sustain adequate numbers of prey species for large predators such as lion and spotted hyena.

One of the rare and threatened plant species of Marakele is the Waterberg cycad (Waterbergbroodboom) Encephalartos eugene-maraisii. The naturalist, author and poet Eugene Marais lived in the Waterberg for 16 years and this cycad was named in his honor. This cycad is endemic to the Waterberg region and grows to 5 m tall among low shrubs at an altitude of 1 450 m.

From its Waterberg Cycads to Yellow-woods and Camel Thorns, Marakele National Parks supports about 765 plant species.

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