Lactobacillus sp., Acetobacter sp. and yeast were the most dominant organisms in the EM stock culture and subculture product. Lactic acid bacteria and yeast were able to grow in the fermentation process utilizing seawater. EM treatment of higher concentrations using EM stock culture and EM clay balls (1% or 4%) contributed to an early removal of malodor and an increase of DO in the polluted sediments, indicating an odor-removing activity of EM. The EM treatment of higher concentrations (1% or 4%) somewhat appeared to modify the microbial communities within the sediments, which was confirmed by existence of a few unique fragments from the stock culture based on PCR-DGGE. It still remains to be elucidated that EM cultures were directly involved in the malodor removal and potential sediment bioremediation.