Prebiotics are non-digestible food components that benefit the host by selectively stimulating the growth and activity of beneficial gut microbiota. Algal polysaccharides, such as fucoidan, alginate, agar, carrageenan, and xylan, are complex carbohydrates derived from marine algae and have garnered significant attention for their potential prebiotic effects, as well as other bioactive properties. Generally, these polysaccharides are resistant to human digestive enzymes and thus reach the colon, fermented by specific gut microbiota, promoting the growth of beneficial bacteria such as bifidobacteria and lactobacilli. The fermentation of these non-digested polysaccharides produces short-chain fatty acids (SCFAs) like acetate, propionate, and butyrate, which play pivotal role in maintaining gut homeostasis, enhancing epithelial barrier integrity, modulating immune responses, and reducing inflammation. In addition to promoting beneficial gut bacteria, algal polysaccharides have been found to boost overall microbial diversity, suppress harmful pathogens, and support the body’s mucosal immune defenses. Their natural antioxidant, antimicrobial, and anti-inflammatory properties make them especially promising as ingredients in functional foods aimed at improving gut health and overall well-being. This chapter highlights the role of algal polysaccharides in modulating the gut microbiome and their associated health benefits, particularly in the context of gastrointestinal diseases such as inflammatory bowel disease (IBD), underscoring their promise as functional ingredients for improving gut health and preventing related disorders.