Over 30% of the 7,400 languages in the world will no longer be spoken by the end of the century. So far, however, our understanding of whether language extinction may result in the loss of linguistically unique knowledge remains limited. Here, we ask to what degree indigenous knowledge of medicinal plants is associated with individual languages and quantify how much indigenous knowledge may vanish as languages and plants go extinct. Focusing on three regions that have a high biocultural diversity, we show that over 75% of all 12,495 medicinal plant services are linguistically unique—i.e., only known to one language. Whereas most plant species associated with linguistically unique knowledge are not threatened, most languages that report linguistically unique knowledge are. Our finding of high uniqueness in indigenous knowledge and strong coupling with threatened languages suggests that language loss will be even more critical to the extinction of medicinal knowledge than biodiversity loss.