World-renown palm and cycad collections include a representation of the world's species.  There are more than 1,500 palm accessions planted in the garden, with 193 genera and more than 500 identified species represented and 3,587 plants.  The palm collection includes the largest number of highly threatened palm taxa of any botanical garden in the world.  Fairchild holds a NAPCC collection of Palms and Cycads. The North American Plant Collections Consortium (NAPCC) is a network of botanical gardens and arboreta within the American Public Gardens Association (APGA) working to coordinate a continent-wide approach to plant germplasm preservation, and to promote high standards of plant collections management.

Fairchild Tropical Botanic Garden's cycad collection includes representations of many of the world's 315 species and is one of the world's largest and most diverse collections with more than 700 accessioned plants.  All cycads are considered to be threatened with extinction.

Rare and endangered species collections include about 4,000 plants of about 100 endangered, threatened or rare species from South Florida and the Puerto Rican archipelago, 15 of which are federally listed as endangered. The collection serves as an important safeguard against extinction and a resource for research, education and natural areas management. Fairchild Tropical Botanic Garden is an affiliate of the Center for Plant Conservation, a national organization dedicated to the preservation and conservation of endangered U.S. species. In addition to conserving ex situ collections of endangered plants, the garden is active in propagating those plants, reintroducing seedlings into the wild and monitoring their long-term success.

Fairchild's Tropical Fruit Program includes an internationally significant collection with more than 500 cultivars of superior tropical fruits such as mango, canistel,  jackfruit,  avocado, and spanish lime. Other special plant collections include a wide diversity of plants from tropical and subtropical climates, including tropical flowering trees, bamboos, tropical vines, arid plants, hibiscus, Bahamian plants and mangroves.

The Fairchild herbarium is the largest in the region with more than 165,000 preserved plant specimens. Strengths of the collection include the floras of Florida, the Bahamas and Caribbean basin; cultivated plants of tropical Florida, and worldwide palms and cycads. The associated taxonomic and ecological reprint collection is one of the largest compilations of botanical literature in the southeastern U.S.; related collections include more than 1,000 original technical botanical illustrations. The Botanical Resource Center, and Virtual Herbarium launched in January 1999, make the herbarium specimens and the garden's living collection accessible via the World Wide Web.