Anti-bacterial activity was evaluated in different crude extracts of five commercially important edible marine bivalves, namely Meretrix casta (Chemnitz), Polymesoda (Geloina) P. erosa (Solander), Perna viridis (Linnaeus), Crassostrea gryphoides (Schlothim) and Villorita cyprinoides (Grey), collected from the coast of Goa (India). Three different procedures, viz. methanol (MeOH), PBS and acid-enzyme hydrolysis (AEH), were used to prepare the extracts. The efficacy of the extraction procedure was assessed on the antimicrobial activity. Antimicrobial assay was carried out against 8 bacterial strains (3 gram positive and 5 gram negative bacteria) and 1 species of fungi. The AEH extracts showed higher activity against the tested organisms as compared to MeOH and PBS extracts. The findings of the present study confirmed that the antimicrobial activity in bivalves appeared to be dependent on the extraction process. Considerable interspecies variation was also observed.