In this study, we focused on natural water-soluble antioxidants from the Jeju benthic diatoms, Achnanthes longipes, Navicula sp. and Amphora coffeaeformis. They were prepared by enzymatic digestion using five carbohydrases (Viscozyme, Celluclast, AMG, Termamyl and Ultraflo) and five proteases (Protamex, Kojizyme, Neutrase, Flavourzyme and Alcalase) and their potential antioxidant activity was assessed. Among the enzymatic digests, Neutrase digest from A. coffeaeformis exhibited the highest effect in DPPH radical scavenging. Flavourzyme (48.7%), Viscozyme (47.4%) and Celluclast (45.7%) digests from Navicula sp. exhibited higher $O^{{cdot}-}_2$ radical scavenging activity. Viscozyme digest from A. coffeaeformis (45.9%) possessed the highest effects in hydroxyl radical scavenging. Termamyl (89.3%) and Protamex (88.8%) digests from A. coffeaeformis had strong metal chelating activity. Lipid peroxidation was significantly inhibited in Termamyl and Kojizyme digests from A. longipes, AMG and Termamyl digests from Navicula sp. and Kojizyme digest from A. coffeaeformisi. These data suggest that enzymatic digests of the Jeju benthic diatoms might be valuable sources of antioxidant which can be applied in food and pharmaceutical industry.