In order to investigate the spatial variations of the over-winter cyanobacteria in different areas of Lake Taihu, sediment and water samples were collected monthly in 14 sites in winters from 2007 to 2008. The phycocyanobilin concentration (PC) of samples was measured by the fluorometry analysis of pigments to confirm the difference of PC's spatial variations among three areas of Lake Taihu. The result shows that, differing from summer, the winter PC in both sediment and water from northern part was lower than western and southern part of Lake Taihu. Even in December, in some parts of western and southern areas the cyanobacteria was still blooming, and PC of surface sediment was also high. According to the result, it is clear that the over-winter cyanobacteria was mainly distributed in western and southern areas of Lake Taihu during the investigation winter seasons.