Several basidiomata of the genus Moniliophthora were found on plant debris, from the bed of the Indus River, Kot Addu, and an irrigated plantation in Chichawatni, Sahiwal, Pakistan. The morpho-anatomical examination along with phylogenetic analyses support the independent position of Moniliophthora purpurensis and M. capitata within the genus Moniliophthora. M. purpurensis is characterized, by an umbilicate and purplish pileus, bifurcate cheilocystidia, long pileal hairs, and lanceolate, lageniform-pedunculate caulocystidia. M. capitata is characterized by having a conical to applanate, dark brown stipe base, polymorphic caulocystidia, and the presence of a conical cap on terminal hair elements of pileus. We present the two new species with illustrated descriptions, molecular analyses, and comparison with morphologically similar or phylogenetically related species.