Polygala spatulata Y. Nong & Run Hua Jiang (sect. Pseudosemeiocardium, Polygalaceae), a new species from a karst cave in west Guangxi, China, is described and illustrated. This new species resembles Polygala isocarpa Chodat in its annual habit, terminal racemes, lamellate appendage, yellow flowers and glabrous seeds, but it can be easily distinguished by its sparsely white-pilose stem and leaf blades, spoon-shaped inner sepals, ovate outer sepals (ca. 1.5 mm) which is glandular and all persistent after anthesis, as well as its elliptic, reticulate seeds. Photographs, an illustration, a distribution map and a comparative table with the most similar species are also provided.