Antioxidants are chemicals that deactivate cell-destructive free radicals. Polyphenols, a class of compounds that exhibit antioxidants properties, can be found in the leaves and stem of some plants. Ipomoea aquatica Forsk. (Water spinach) contains polyphenols that exhibit antioxidants activity. Based from the earlier studies of water spinach, it contains phenolic compounds that are responsible to the overall antioxidant activity. Most phenolic compounds can be found in leaves and stem of water spinach. This study aims to identify the presence of functional groups using Fourier Transform Infrared Spectrometer and to determine the total phenolic content of leaf and stem extracts of water spinach. Infrared spectroscopic analysis showed that the crude extract of water spinach leaf has alcohol, amines, and cyclic amines based on the broad peak found between 3,500 to 3,000 cm-1. The stem extract shows the presence of phenolic compounds based on the peaks from 2,950 to 2,800 cm-1. This denotes that it has antioxidant activity. The total phenolic composition of the stem extract is higher having the mean of 82.3 GAE/mL (Gallic acid equivalent/milliliter) while leafextract has 64.75 GAE/mL. In free radical scavenging activity with DPPH, the stem has a greater antioxidant action ranging from 3.03 to 58.82% while the leaf extract has 9.72 to 20% scavenging effect. Statistical testing showed that there is no significant difference in the percentage of free radical scavenging activity.