Low molecular weight peptides are among the most active bioactive components that have been isolated from marine molluscs. Currently, peptides isolated from molluscs as well as their synthetic structural analogues are in clinical trials as anticancer compounds and have been approved for use in pain management. These Bioactive peptides have also been demonstrated to exhibit antioxidant activities. This study aimed at isolating and profiling the low molecular weight peptide fractions from extracts of two common marine molluscs; P. aurita and T. fuscatus obtained from the Niger-Delta region of Nigeria. This study also investigated the free radical scavenging activity of the isolated fraction. Fourier Transform Infrared Spectroscopy analysis was carried out to determine the chemical entities and common functional groups found in the extracts. The Low molecular weight peptides were isolated using Molecular sieve chromatography, while the peptide profiles were established using SDS-PAGE and Thin Layer Chromatography (TLC). The free radical scavenging potential of the peptides was also assessed qualitatively using TLC, with DPPH as stain. The results show the presence of several low molecular weight peptides in the extracts of both P. aurita and T. fuscatus. Yellow spot on a purple background, indicating antioxidant activity was observed in the TLC plates sprayed before the chromatographic run. This activity was lost on further separation, indicating a synergistic effect. Further studies to effectively separate these fractions into individual peptides, investigate the synergistic effect observed as well as further explorations of possible bioactivity of these peptides is required.