Indigofera jintongpenensis, a new species of the subfamily Papilionoideae of Fabaceae, is described and illustrated from Yunnan, southwest China. The new species is characterised by having a prostrate habit, flexible stems and branches, as well as spreading, sub-basifixed, asymmetrically 2-branched trichomes covering the entire plant, discoid calyx, and racemose inflorescences 6–8-flowered, short, 1–2 (–3.5) cm in length, apparently shorter than the leaf. A distribution map and comparison of morphological diagnostic characters with its morphologically similar species are provided. Additionally, a preliminary conservation assessment of I. jintongpenensis is proposed following IUCN criteria.