Marine polychaete is an important component in marine benthic communities and can be widely found in Malaysia. To date, the information regarding its chemicals and biological activities of marine polychaete is still limited. This study aims to evaluate the chemical fingerprint of the marine polychaetes Marphysa moribidii and Diopatra claparedii using Attenuated Total Reflectance Fourier-Transform Infrared (ATR FTIR) metabolomics. The antioxidant activity including total phenolic content (TPC) and DPPH free radical scavenging activity was also evaluated. The results showed that D. claparedii has a higher amount of TPC (0.47±.0.03 mg GAE/g) compared to M. moribidii (0.30± 0.01 mg GAE/g). The DPPH activity tested at the concentration 5000 µg/ml showed percentage of inhibition expressed by D. claparedii and M. moribidii extracts were 38.8011.70 and 25.547.35 respectively. The principal component analysis (PCA) score plot showed distinct clusters between M. moribidii and D. claparedii. Further investigation via PCA loading plot showed that the FTIR signals at 3340, 1090, 1047 and 880 cm-1 were contributed by D. claparedii. Meanwhile, the partial least square (PLS) analysis revealed several signals were correlated with the TPC including stretching vibration of C-H at 2854 cm−1, C=C bonds at 1640 cm-1 and C=C bending at 1726 cm-1 showing the presence of aromatic ring deformations. This study provides the key important chemical fingerprint of different marine polychaetes (D. claparedii sp. and M. moribidii sp.) that might be useful for the discovery of bioactive compounds from natural resources.