Effect of mucus bacterium on the permeability of mortar and the microstructure of mortar surface was investigated. Mortar samples were separately immersed in sterilized seawater, 2216E culture medium and 2216E culture medium containing mucus bacterium for 154days. The chloride content in different layers of mortar and pH value of immersion solution were measured for evaluating effect of microorganism on mortar permeability. Experimental results indicate that the bacteria positively decelerates the penetration of chloride into the mortar and inhibites the dissolution of calcium hydroxide in mortar. The microstructure observation shows that a biofilm with rod shaped bacteria is covered on the surface of the mortar sample immersed in 2216E culture medium containing mucus bacterium. Biofilms may be the major factor that inhibits the chloride permeating into mortar and leaching out of OH- from mortar.