The aim of the study was to investigate the amino acid composition of five species of brown macroalgae of the genus Cystoseira (C. corniculata, C. compressa, E. amentacea, G. barbata and C. spicata) in order to determine the potential application of the proteins of the aforementioned algae in food, cosmetic and/or or the pharmaceutical industry. The protein content was determined indirectly from the amount of nitrogen using the Kjeldahl method, and the composition and content of amino acids in the tested samples of brown macroalgae was determined using the HPLC method with a fluorescence detector. The protein content in the selected macroalgae species of the genus Cystoseira ranged from 5.35 to 6.79%, and the highest content was measured in the macroalgae C. compressa, and the lowest in G. barbata. The ratio of essential to non-essentail amino acids (EAK/NEAK) was in the range from 0.15 to 0.82, which indicates that the NEAK content was higher compared to EAK in all tested species. The highest ratio was measured in the macroalgae C. compressa, which indicates a higher content of essential amino acids compared to the other examined macroalgae, and the lowest in E. amentacea. The most abundant non-essential amino acids in all analyzed macroalgae were aspartic and glutamic acid, alanine and glycine, and from essential amino acids histidine, phenylalanine and threonine.