Aims This study discusses the effect of phenolic compounds extracted from brown seaweed (phlorotannins) on mixed microbial cultures found in anaerobic systems. Methods and Results Assays were conducted with phloroglucinol as the nonpolymerized form of phlorotannin and with phlorotannins extracted from the brown seaweed Laminaria digitata. Electron micrographs revealed that phlorotannins induce significant extra- and intracellular effects upon cells, with the disruption of cell membranes observed with most micro-organisms. Microscopy results were further confirmed by cell membrane leakage assays demonstrating that phloroglucinol strongly affects cell membrane permeability. However, cell membrane leakage could not be observed with phlorotannins as the cell suspension immediately started to coagulate and impaired spectrophotometric measurements. Conclusions Results suggest that the bactericidal activity of phlorotannins is a function of the level of polymerization of the compounds. By monitoring intermediary compounds during the anaerobic digestion of phlorotannins, it was also found that higher energy consumption is required by micro-organisms for survival under stress induced by phlorotannins. Significance and Impact of the Study The successful anaerobic degradation of brown seaweed is thus likely to be dependant on the concentration of phenolic compounds present and their bactericidal effect on micro-organisms. This is the first article to posit a probable mode of action for the antimicrobial effect of phlorotannins.