The Yucatan Peninsula possesses a unique climate, geology, landscape, and biota that includes a distinct flora of over 2300 species; of these, close to 800 plants are used in what is known as Mayan traditional medicine, and about 170 are listed as native or endemic. Even though the flora of the Yucatan peninsula has been widely studied by naturalists and biologists, to date, phytochemical and pharmacological knowledge of most of the plants, including the medicinal plants, is limited. Presently, phytochemical studies carried out on plants from the Yucatecan flora have resulted in the identification of a wide variety of natural products that include flavonoids, terpenoids, polyketides, and phenolics with cytotoxic, antiprotozoal, antibacterial, anti-inflammatory, analgesic, antioxidant, and antifungal activities. This review describes the main findings in over 20 years (1992 to 2018) of exploring the natural product diversity of the Yucatecan flora.