The Meretrix meretrix is abundantly present in the Indian coastal areas which can be used as an important useful bioactive source for industrial applications. The M. meretrix visceral mass (MMV) was hydrolysed with four different enzymes and verified for anti-inflammatory activity with the help of HRBC membrane stabilization (HMS) and albumin denaturation (AD) assay. Among the hydrolysates, the tryptic 6th hour hydrolysate was selected for purification using ultrafiltration and size-exclusion chromatography (SEC). Further, the purified peptide was identified to have six amino acid sequence (HKGQCC, 675.582 Da). However, to confirm the anti-inflammatory effects of the purified peptide, it was investigated for nitric oxide synthase (iNOS), pro-inflammatory cytokines production as well as cyclooxygenase-2 (COX-2) activation in lipopolysaccharide (LPS)-stimulated RAW264.7 cells and also evaluated for its functional properties. The in-vitro gastrointestinal digestion was performed on the peptide which cleaved the peptide into two i.e. MMV1 (HK, 284.1 Da) and MMV2 (GQCC, 410.1 Da). The data suggested that the MMV2 peptide have maximum activity and was found to be stable at high temperatures. The MMV2 peptide demonstrated abrupt localization throughout the adult zebrafish body and successfully downregulated the mRNA levels of inflammation-related genes in LPS-induced adult zebrafish. This study indicates that the peptide MMV2 possesses anti-inflammatory activity by suppressing the induced inflammation and can be a strong competitor against non-steroidal anti-inflammatory drugs (NSAIDs).