Studies on the size fractions of plankton communities in large shallow lakes are rare. Here we report on size fractionated plankton communities from Lake Taihu based on bimonthly measurements in field from October 2002 to September 2003. Based on the diameter(R) of the plankton community we analyzed size fractions of R ≥ 41 μm, 2 μm ≤ R < 41 μm and R < 2 μm. The fraction larger than 41μm, represented mainly by Microcystis colonies, dominated in Meiliang Bay. The respiration of this fraction contributed over 70% to the total plankton community respiration, while the fraction < 2 μm(mainly bacteria) contributed about 18% of the total plankton community respiration. In the center of the lake, the plankton community with R ≥ 41 μm contributed about 10% to the total plankton community respiration, while the plankton community R < 2 μm contributed about 65% to the total plankton community respiration. For the whole lake, the plankton community with R ≥ 41 μm, particularly the Microcystis colonies, dominated total plankton community respiration in the northern part of the lake while bacterial respiration was most important in the center of Lake Taihu.