The relationship between bacterioplankton and phytoplankton community composition was investigated from April to June, 2005 with samples taken at five different stations in Lake Taihu. Bacterioplankton and phytoplankton community composition as determined by denaturing gradient gel electrophoresis of polymerase chain reaction amplified bacterial 16S rRNA gene fragments (PCR-DGGE) and microscopic examination respectively, revealed a high degree of diversity. In total, 43 unique bands were identified among those DGGE profiles, and 29 dominant phytoplankton populations were observed. The DGGE profiles were clustered into two distinct groups. These two clusters were closely associated with two dominant phytoplankton, Ulothrix sp. and Microcystis spp. as observed on April 19^th and on May 27^th and June 27^th, respectively. The relationship between bacterioplankton and phytoplankton community composition was investigated using Canonical Correspondence Analysis (CCA) with Shannon-Wiener diversity index of phytoplankton community (H_p), total cell abundance of phytoplankton (N), and the relative abundance of Microcystis spp. (M) as the variables. The CCA results indicated a 30.9% correlation coefficient suggesting a high degree of correlation between bacterioplankton community composition and the phytoplankton community.