The objective of the present work is to isolate the phytoconstituents from the active extract of Aponogeton natans (Linn.) Engl & Krause leaf with leaf stalks. The preliminary phytochemical screening and HPTLC analysis were carried for the pet ether, benzene, chloroform and methanol extracts. From the preliminary phytochemical and HPTLC analysis it was found that methanol extract contained carbohydrate, protein, phytosterol, glycoside, saponin, flavonoids and polyphenols. The methanol extract showed 11 peaks having maximum Rf value 0.08, 0.12, 0.18, 0.27, 0.38, 0.47, 0.53, 0.56, 0.62, 0.73 and 0.80. Thereafter the methanol extracts was subjected to column chromatography for the isolation of the phytoconstituents. Two compounds namely ANSD-1 and ANSD-2 were isolated and purified from methanol extract by column chromatography and the structure were determined as stigmasterol and gallic acid by physical, chemical and spectral characteristics. The information gathered from the phytochemical study and HPTLC of Aponogeton natans Linn. delivered the parameters will serves determine the quality of the plant material in the future. The isolation carried determined the presence of two important phytoconstituents of medicinal value which may be responsible for the pharmacological action of the plant.