Polystichum perpusillum L.B. Zhang & H. He, a new fern species of Polystichum sect. Haplopolystichum (Dryopteridaceae), is described and illustrated from the entrance to a karst cave in southern Guizhou, China. A phylogenetic analysis based on the chloroplast trnL-F sequences shows that it is phylogenetically isolated in the section with no close relatives. Morphologically, it is similar to P. minutissimum, but P. perpusillum has an acute lamina apex, up to 12 pairs of pinnae per lamina, and deltoid-ovate or ovate-lanceolate rachis scales, while P. minutissimum has a round lamina apex, 5–8 pairs of pinnae per lamina, and subulate or linear rachis scales. Polystichum perpusillum has a granulate sculpture with Verrucae on its perispore, a sculpture rare in the genus. The species is considered to be critically endangered.