Biopigments known as a colored substance that is commonly generated by the plant also has the primary function of photosynthesis. In addition, the biopigments containing networks of conjugated double bond are potential for antioxidant as they can donate one or more electrons to free radicals. Aims: The antioxidant activities of biopigments isolated from diatom Navicula sp. was examined against 2, 2-diphenyl-1-phycrylhydrazil (DPPH) radicals. Methods: The diatom Navicula sp. was cultured in the seawater medium enriched by urea, phosphate, silicate and iron; the biopigments were isolated from dried algal biomass using acetone as a solvent; biopigments purified by a silica column chromatography with n-hexane: acetone (8:2) (v/v) as solvent; the purified biopigments were characterized by Visible spectrophotometer and 2D Thin Layer Chromatography (TLC); and the antioxidant activities of biopigments was assayed against DPPH radicals, with ascorbic acid used as a control. Results: The cell density of Navicula sp. of 2.56 g/L was observed on the 5th day. There were 6 biopigments showing characteristics of absorption spectrum at 350–800 nm identified as β-carotene, chlorophyll a, pheophytin a, diatoxanthin, diadinoxanthin and fucoxanthin. The antioxidant activity of ascorbic acid, crude extract, pheophytin a, fucoxanthin and β-carotene against DPPH radicals assign an IC50 values of 4.9; 107.4; 27.1; 23.3 and 5.32 µg/mL respectively. Conclusion: Both crude extract and pure biopigments isolated from Navicula sp. exhibited DPPH radical scavenging.