Algae growing in an enclosed sea may inhibit eutrophication because they absorb nutrients in the water. However, dead algae often cause anaerobic conditions in the water just above and on sediment after they are deposited on the bottom. We found that Stichopus japonicus inhibited the anaerobic processes coupling water sulfite production in sediment. The present study investigates whether S. japonicus inhibits algal flourish and influences sediment properties such as organic matter contents. Aquarium experiments were carried out at Komatsushima port in Tokushima Prefecture, western Japan. The aquaria used in the experiments were supplied with water directly from the adjacent sea (6 L/min), laid with sand of 10 cm depths, and lighted at 12 h intervals. Six aquaria each containing a sea cucumber from Komatsushima port and six aquaria without any were used in the experiments. Water temperature ranged between 9 and 15 degrees C during December 2000 and April 2001. Salinity ranged between 32 per thousand and 34 per thousand. Algae began to cover the bottom of the aquaria without S. japonicus after 2 weeks, whereas no growth was evident in the aquaria containing sea cucumbers. Chlorophyll a concentration in the surface sediment of the aquaria with S. japonicus (6.1+/-3.6 microg/g, mean S.D.+/-standard deviation) was significantly lower than that without it (60+/-17 microg/g, U-test, p<0.05). Phaeophytin concentration in the surface sediment of the aquaria with S. japonicus (0.9+/-0.09 microg/g) was also significantly lower than that without it (4.5+/-1.0 microg/g, U-test, p<0.05). TOC concentration in the surface sediment of the aquaria with S. japonicus (2.6+/-1.3 microg/g) was slightly lower than that without it (4.0+/-1.2 microg/g). These results showed that algal biomass and organic matter concentration of the bottom were decreased in the presence of S. japonicus. Therefore, S. japonicus inhibits algal bloom and decrease the contents of organic matter deposited on the bottom of enclosed sea areas.