<p>Over the years, brown algae have been highlighted as valuable natural sources of bioactive polysaccharides. They are known to consist of a number of bioactive polysaccharides, fucoidan being the principal polysaccharide. Fucoidans, a sulphated polysaccharide composed of a fucopyranose backbone and several monosaccharaides have been reported to possess numerous biological activities such as anticancer, antioxidant, antiviral, antithrombotic, and anti-inflammatory properties, thus may confer health benefits to humans. However, the main mechanisms bridging the structural complexity of fucoidans and their biological activity are mostly unexplored. This study aimed to compare the structural features and the antimicrobial properties of the fucoidan extracts isolated from the two brown macroalgae, <i>Fucus vesiculosus</i> and <i>Saccharina latissima</i>, sampled in the littoral zone of the Barents Sea. The physicochemical properties of fucoidans and their polyelectrolyte properties were investigated. The antibacterial activity of fucoidans was evaluated using the disc diffusion method against <i>Bacillus subtilis</i> (gram-positive bacteria), <i>Pseudomonas aeruginosa</i>, and <i>Proteus mirabilis</i> (gram-negative bacteria). It was shown that fucoidans inhibited the growth of both gram-positive and gram-negative microorganisms. At the concentration of 0.25–0.5%, the highest clear inhibition zones were observed for all the studied bacteria. The high antibacterial activity of fucoidans was due to the availability of functional groups and the particle sizes of fucoidan molecules that affect the cell membranes of the bacterial microflora. On the basis of obtaining results, fucoidans were suggested as potential natural and green bactericidal agents to be used by the pharmaceutical, medicine, and food industries.</p>