Vertical profiles of chlorophyll concentration, salinity, water temperature, illuminance and phytoplankton species composition in Lake Shinji were surveyed in November 11 1999. The chlorophyll concentration determined by spectral absorption method was the highest at surface. Determined by in vivo method, in contrast, the concentration at the surface was less than that in the lower water column. Probably in vivo method was not able to detect the high concentration of Microcystis sp. at the thin surface layer. Relatively high chlorophyll concentration determined by in vivo method in the lower water column was possibly caused by low phytoplankton activity.