Two new species, Phlegmariurus iminii Kiew (Lycopodiaceae) from limestone karst and P. monticola Kiew from montane habitats, are described from Peninsular Malaysia and a new combination is made for Phlegmariurus pinifolius (Trevis.) Kiew. Phlegmariurus iminii, 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.