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The reserve houses a tropical dry forest ecosystem, within the reserve the flora consists of over 500 species of plants and tropical dry trees, such as pochote, black rosewood, mahogany, hogplum and guacuco, as well as a large variety and amount of orchids.
It incorporates beaches, fog forest, dry forest, small islands and two larger islands, Salango and Isla de la Plata, the latter named for a legendary hoard of silver left by Sir Francis Drake.
The Northwestern thorn scrub forests are thought to be tropical dry forests that have been degraded through intensive agriculture and grazing into stunted and open thorn scrub, dominated by trees such as Acacia senegal and Acacia leucophloea, as well as Prosopis cineraria, Capparis zeylandica, and species of Salvadora, Gymnosporia, Grewia, and Gardenia.
The upper basin was formerly covered by tropical dry forest, thorn forest, and xeric shrublands.
Indian sandalwood (S. album) is found in the tropical dry deciduous forests of India, the Lesser Sunda Islands of Indonesia, and Arnhem Land of northern Australia.