Two new species, Phlegmariurusiminii Kiew (Lycopodiaceae) from limestone karst and P.monticola Kiew from montane habitats, are described from Peninsular Malaysia and a new combination is made for Phlegmariuruspinifolius (Trevis.) Kiew. Phlegmariurusiminii, known from a single hill threatened by quarrying, is Critically Endangered; while P.monticola and P.pinifolius that are relatively widespread are of Least Concern.