In the biological sciences the use of medicinal plants in indigenous cultures is commonly seen as being based on a long tradition ('traditional medicine'). However, under normal circumstances, ethnobotanical studies cannot provide evidence on the antiquity of specific uses for medicinal plants since oral traditions have a limited historical depth and archaeological evidence does not provide evidence for the specific medicinal use of a certain plant. Here, we provide evidence for the antiquity of medicinal plant use in the Olmec region in Mexico by comparing the pharmacopoeias of the linguistically related Lowland Mixe and Zoque-Popoluca. These cultures, separated for about 2000 years, have cognates for vernacular medicinal plant names in common. For fifteen species such cognate names were detected. Also, a statistically significant segment of the medicinal flora is used for similar purposes. Overall, 123 species are shared between the two groups and of these 62 have a similar usage. In nine cases they also have a similar name. These findings make a transmission of such knowledge since the time of the Olmecs highly likely.