Seaweeds are rich sources of polyphenolic chemicals, particularly tannins, which are becoming well-known for their possible antibacterial and prebiotic qualities. Tannins are isolated and described in this work from a few species of red and brown seaweed. Their impact on the makeup and activity of the human gut microbiota is then evaluated. The tannins were extracted by the use of aqueous and organic solvents, and their quantification was done by the use of Folin–Ciocalteu and protein precipitation procedures. Mass spectrometry and high-performance liquid chromatography (HPLC) were used to identify the tannin ingredients. In vitro fermentation models repeated the human colon, which was used to test the effects of tannin exposure on microbial diversity by the use of 16S rRNA gene sequencing. The results showed that tannins produced from seaweeds decrease aggressive pathogens like Enterobacteriaceae and upgrade beneficial bacterial species like Bifidobacterium and Lactobacillus, hence modulating the gut microbiota. Additionally, the production of short-chain fatty acids (SCFAs) was positively affected, which indicates improved colonic health. These results suggest that seaweed tannins could be useful bioactives for regulating the gut microbiota, which calls for more research into their potential application in dietary modifications and gut health treatments.