His research focused on the high-elevation páramo and sub-páramo regions of the Andes Mountains in South America, especially the flowering plant families Asteraceae and Malpighiaceae.

He played an important role in the founding of the Organization for Flora Neotropica.

[1] In 1997, the Smithsonian Institution established the José Cuatrecasas Botanical Fund to "support significant research projects that emulate the spirit of the research of José Cuatrecasas".

The Smithsonian also awards a José Cuatrecasas Medal for Excellence in Tropical Botany annually.

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