Watermelon (Citrullus lanatus) fruit, which is a seasonal fruit, is a good source of valuable components. Peel, rind and seeds which are the major by-products of watermelon fruit processing industries, are good sources of nutrients, fibre, pectin and phytochemicals. Pectin was extracted from watermelon fruit peel and rind and also from citrus peel for comparison studies. The influence of extracting medium and isolating solvent was studied by using ethanol and acetone independently to know their efficiency. Physical and chemicals properties were studied for the extracted pectin from peel and rind and compared with the citrus and commercial pectin properties. FT-IR analysis was performed to the pectin extracted from peel and rind to determine the function groups present in them. Scanning Electron Microscopy (SEM) analysis was carried out to study the morphology of extracted watermelon fruit peel and rind pectin. Results showed that citric acid extraction along with ethanol gave the highest yield of pectin when compared with acetone. The pectin content ranged between 15-20%. The extracted pectin quality was comparable with that of the commercial pectin. It was observed that the FT-IR spectra of both the pectin samples had characteristic peaks at 3420.9, 2936.8, 1739 and 1082.9 cm-1 corresponding respectively, to –OH, -CH, C=O of ester and acid, and –COC- stretching of the galacturonic acid. It could be concluded from the above investigation that good quality pectin can be extracted from the peel and rind using citric acid as an extracting media and ethanol as a precipitating solvent. Recovery of valuable by product pectin from fruit peel and rind not only reduces the waste disposal and environmental pollution but also offers great scope for utilization in development of many functional foods.