The intestine is the natural habitat for a large and dynamic bacterial community, which perform vital metabolic and immune functions that significantly effect the nutritional and health status of the host. The major physiological functions of intestinal flora include metabolic activities that lead to important trophic effects on immune structure and function as well as protection of the colonized host against invasion by transient microbes. The intestinal flora is both a target for nutritional intervention and a factor influencing the biological activity of food compounds acquired orally. Marine environments, as a source of diverse organic compounds, can supply us with a number of beneficial and health-promoting ingredients. This review focuses on the physiological functions of intestinal flora and reciprocal interactions between intestinal flora and dietary marine components including polysaccharides, lipids, protein, taurine, carotenoids, minerals, and polyphenols. This review can serve as a valuable reference regarding the consumption of seafood and marine nutraceuticals.