Marine lipids contain eicosapentaenoic acid (EPA) which has anti-inflammatory effects. The aim of this research was to study, using the dextran sulfate induced acute colitis (AC) model, the effect of an EPA-rich shark fin supplemented diet on the mucosal lipid composition. The histology score increased in AC (p < 0.05), but only slightly in the EPA group. Similarly, colonic permeability to a intraluminally instilled water-soluble contrast medium significantly increased in the AC group, but not in EPA group. As compared with controls, the AC group showed lower levels of phosphatidylethanolamine, phosphatidylinositol, free fatty acid C20:5, and PL-FA C18:1 and C18:2 and higher levels of sphingomyelin, lysophosphatidylcholine, and C18:1 and free fatty acid C20:4 (p < 0.01) after 2 and 7 days. In the EPA group sphinogmyelin and lysophosphatidylcholine slightly increased and free fatty acid C20:4 decreased (p < 0.05) after 7 days, and no PL-FA change occurred. This study confirms the protective properties of EPA-rich marine food. EPA-enriched diet is protecting the colonic mucosa from the early derangements of lipid components occurring in this experimental AC model. This effect is likely to contribute to maintain an effective mucosal lining barrier.