Nannochloropsis sp., is one of the microalgae that produces important antioxidants. We postulate that the presence of phenolic compounds in the methanolic extract of Nannochloropsis sp. exhibits preventive effect against DNA damage induced by 100 µM concentration of hydrogen peroxide (H₂O₂) in L929 cells. High performance liquid chromatography (HPLC) analysis revealed that Nannochloropsis sp. methanolic extract contained antioxidant compounds such as p-coumaric acid, caffeic acid, naringenin and hesperitin. In this study, we utilised comet assay to measure the activity of DNA damage induced by H₂O₂ in L929 cells and the preventive effect of Nannochloropsis sp. methanolic extract and caffeic acid. After 24 hours of treatment, 100 µM of H₂O₂ induced 64.4 ± 4.6% of DNA damage in L929 cells compared with the untreated cells (p < 0.05). Interestingly, the scale of DNA damage induced by the H₂O₂ was reduced to 46.3 ± 12.7% when treated with 0.4 mg/mL of Nannochloropsis sp. methanolic extract (p < 0.01). The DNA damage was further reduced to 7.3 ± 2.9% when treated with 20 µM of caffeic acid (p < 0.01), a compound found in the microalgae extract. In conclusion, Nannochloropsis sp. methanolic extract which contained phenolic compounds, was able to protect L929 normal cells from oxidative DNA damage and therefore may confer protection from genetic mutation and cancer formation.