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Knowledge about the therapeutic properties and efficacy conferred by several plants to indigenous communities is based on observations, traditional knowledge, and forms of use or application within local, cultural, and territorial contexts. However, to some extent, favorable responses to these plants depend on the form in which a plant is used and its phytochemical composition. This work aimed to evaluate the contents of total polyphenols and flavonoids and antioxidant activity and determine qualitative phytochemical profiles of T. lucida, T. lunulata, C. mexicanum and C. macrostemum from samples of plants collected in four indigenous regions of Oaxaca, Mexico. The results showed that the contents of phenolic compounds and antioxidant activity differed significantly among the evaluated species and that the effect of species was greater than the ecological-environmental effects caused by the origins of the samples. Tannins, alkaloids, steroids, terpenoids, and coumarins were qualitatively identified in all evaluated species, and emodins were detected only in T. lucida. Among the communities visited, it was documented that all the species are used to treat gastrointestinal disorders, and antimicrobial, calming and anti-inflammatory properties were recorded for all four species. The effectiveness conferred to these plant species in the communities to treat ailments, including endemic diseases, is partly due to the complex phytochemical composition and the beneficial properties released during infusion or decoction.