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Obesity is often caused by high levels of blood fats and can lead to the emergence of chronic diseases such as high blood pressure, coronary heart disease, and type II diabetes. One of the known anti obesity drugs is orlistat, that works as pancreatic lipase inhibitor. Methanol extract and flavonoid isolate from watermelon mesocarp have been shown to have activity as pancreatic lipase inhibitor, but the flavonoid species is not known yet. The aims of this study are to: isolate the flavonoid from ethanol extract of watermelon mesocarp, determine the activity of isolated as pancreatic lipase inhibitor and determine the types of flavonoid isolate spectrofotometrically by UV-Vis, FT-IR, and LC- MS/MS. This descriptive laboratory study using methanol in extraction stage and then TLC to isolate the flavonoid. Inhibitory activity assay have been done by titrimetric method, using porcine pancreatic lipase (Sigma) as enzyme, olive oil as substrate and orlistat as standard inhibitor.The results had shown that: 1) there are six flavonoid isolates from ethanol extract of watermelon mesocarp, that has pacreatic lipase inhibition power: 77 fold (1st and 2nd isolate), 71 fold (3rd isolate), 92 fold (4th isolate), 103 fold (5th isolate), and 96 fold (6th isolate) respectively, relative to Orlistat at the same mass, and 2) based on the spectrum of UV-Vis, FT-IR, and LC-MS/MS, all of the six flavonoid isolates are catechin or oligomer of catechin.