Metabolite profiling is the multi-parallel relative quantification of a mixture of compounds or compound classes using chromatography and universal detection technologies (GC-MS, LCMS) for biological samples. Metabolic profiling could provide the link between traditional herbal medicines and molecular pharmacology. Aegiceras corniculatum is one of the important species of black river mangrove plant. Present studies explaining the strategies of metabolite profiling of polar as well as non-polar compounds from leaves and bark extracts of plant Aeiceras corniculatum by using GC-MS. The range of solvent from non-polar to polar viz. petroleum ether, chloroform, ethyl acetate, methanol and water separately used for extraction. The GC-MS profile revealed the presence of phenolics, carbohydrates, steroids, alkaloids, hydrocarbons, fatty acids and esters, amines etc. In parallel with GC-MS statistical analytical tools such as principal component analysis used to yield significant and precise results. In present study the biologically active compounds-Plectoxanxthin, Ndeacetyl Colchicine, Cyclopentaneundecanoic acid, Thiirane, Gamolenic acid, 8,11,14-Eicosatrienoic acid, Lupol, Rhodopine were reported from different extracts of plant.