For strategic planning of habitat restoration at Tokyo Bay, a basic data set of habitat had been corrected by field work at March and September, 2006. The targeted species are sessile organisms and macro benthos at seawalls and tidal flats. We found 1) even in the inner part of the bay where over eutrophicated area, tidal flats had kept rich benthos diversity, 2) sessile organisms diversity had been attributed by the spatial structure of water quality such as transparency or salinity. A hypothesis of predominant factors for the spatial distribution of benthos and sessile organisms at Tokyo Bay shore is formulated.