Due to the adaption to environmental stress, biomasses of microalgae and cyanobacteria contain high-value pigments and phenolic compounds with antioxidant capacity to be used as ingredients for food, cosmetics, and pharmaceuticals. To expand the current state of knowledge about microalgae and cyanobacteria as sources of high-value compounds biomasses and extracts of 13 microalgal and cyanobacterial species of the four divisions, namely Chlorophyta, Rhodophyta, Cyanophyta and Diatoms, with regards to their antioxidant capacity, were characterized. Moreover, cell disruption prior to extraction of the slurry of the alga Acutodesmus obliquus was investigated for increasing yields of compounds with antioxidant capacity. The total chlorophyll and carotenoids contents of the tested green algae was with up to 60 mg g⁻¹ and 12 mg g⁻¹, respectively, substantially higher compared to the other algae. Results revealed that aqueous extraction is effective for extracting phenolic compounds from biomass. The quantity of phenolic compounds in the extracts revealed no superior species. Nevertheless, Neochloris oleobundans, Phormidium sp., and Wilmottia murravi can be recommended as species with high contents in phenolic compounds (>20 mg gallic acid eq. g⁻¹). Phormidium ambiquum and Phormidium sp. were the strains with highest contents in water-soluble compounds (12–14 μmol ascorbic acid eq. g⁻¹), while N. oleobundans and A. obliquus were the strains with highest contents in lipid-soluble compounds (60–80 μmol trolox eq. g⁻¹). Cell disruption prior to extraction doubled the yields of compounds with antioxidant activity, which underlines the necessity of an effective pre-treatment. Results of this study contribute to the proceeding towards a utilization of microalgal and cyanobacterial biomasses for the formation of high-value compounds with antioxidant properties and potential for food, cosmetic, and pharmaceutical industries.