Macrophytes are the main primary producers of coastal ecosystems, which include many habitat-forming species with vital ecological importance. Macroalgae and seagrasses as any other macroorganisms in this ecosystem are in permanent contact with microbes. Seawater contains millions of microorganisms per ml of bacteria, cyanobacteria, fungi, microalgae and protists (Goecke et al. 2010), which eventually interact with every single species of macrophytes during the entire lifetime till the next generation. In the marine environment microbes are found in the immediate surroundings, fl oating in the water or along with currents and tides. The aquatic environment favors the formation of biofi lms on surfaces. Besides every mechanical, chemical and physical defense, microorganisms can be found on every living surface in the aquatic environment, and this includes marine macrophytes as well (Wahl et al. 2012).