To exploit indigenous microalgae with potential for antioxidant activity, 10 microalgal strains (expressed as genus and species) were isolated from fresh and sea waters in Hainan Province, China, according to their high biomass, strong antioxidant capacity and antioxidant enzyme activity. The strains were identified based on their morphology, 18s rDNA and internal transcribed spacer (ITS) sequence analysis. Five strains were identified as Dictyosphaerium sp. 1A10, Desmodesmus armatus (D. armatus) B38, Masaia oloidia 2Fg, Chlorella vulgaris B43 and Chlamydomonas chlamydogama WC11. Microalgal antioxidant capacity was determined. Dictyosphaerium sp. 1A10 showed the highest superoxide dismutase activity (940 ± 10 U/g tissue), 2,2′-diphenyl-1-picryhydrazyl radical scavenging capacity (100 ± 10%) and oxygen radical absorbance capacity (620 ± 10 μmol Trolox/g); D. armatus B38 showed the highest glutathione peroxidase activity (110 ± 10 U/g tissue), ferrous ion chelating capacity (93 ± 7%) and hydroxyl radical-scavenging capacity (97 ± 2%); Scenedesmus ecornis (S. ecornis) G2 showed the highest 2,2′-azinobis-(3-ethylbenzthiazoline-6-sulphonate) scavenging capacity (92 ± 5%). PCA also suggested that D. armatus B38, Dictyosphaerium sp. 1A10 and S. ecornis G2 with highest comprehensive scores (1.83, 1.23, and 0.59, respectively) could be the most appropriate candidates for antioxidants.