The use of Fourier Transforms Infrared Spectroscopy (FTIR) in screening secondary metabolites provides valuable information on qualitative, quantitative and the pattern of the biologically active compounds. The present study was carried out to identify functional groups present in water, methanol and n-hexane extracts of Allium sativum and Nymphaea lotus. It was revealed that Allium sativum and Nymphaea lotus possess numerous secondary metabolites {A. sativum L. (isothiocynate, acid halide, conjugated aldehyde, imine/oxime, halo compound, conjugated amine, alphaticprimary amine, aldehyde, anhydride, α,β-unsaturated ketone, carboxylic acid, nitro compound, aromatic ester) and N. lotus L. (aliphatic primary amine, halo compound, anhydride, vinyl ether, cabocylic acid, cyclic alkene, unsaturated ketone, aldehyde, aliphatic primary amine, aldehyde, alkane, benzene derivative, sulphide, alkene, akyl aryl ether, sulfonyl chloride, δ-lactone, imine/oxime, thiocyanate, amine salt, esters, alkene, nitro compound, sulphate, sulphone, akyl aryl ether, aromatic ester, fluoro compound, amine salt, sulphonyl chloride, tertiary alchohol, α,β-unsaturated ketone, alkyne, allene, sulfonic acid, α,β-unsaturated ester, alphatic primary amine, amine, sulfonyl chloride, vinyl ether, aromatic amine, alphatic ketone, isothiocyanate, thiocynate, conjugated alkene and anhydride)} that may be biologically active which could be useful in production of antimicrobials and other medicinal products that can be of high benefits in proffering reliable alternative medicine to human and animal diseases.