The fish species richness and abundances were compared between the seagrass beds and the neighoboring bare sand substrata at two sites i.e. Megaura and Yokoyama in Lake Hamana, central Japan from March to May each year in 1998, 1999 and 2000. The species richness in seagrass beds were higher than those in the bare substrata and the species composition and the relative abundance of each species differed between them. The mean numbers of individuals and the species diversity, however, did not differ between the two habitat types. Such phenomena may be due to the seasonal changes in habitat structure of the studied seagrass beds.