Cyanobacteria,specifically Microcystis,usually form massive blooms in eutrophic freshwater lakes.Cyanobacterial samples were collected from eight sites of both Lake Taihu and Lake Chaohu in late summer to determine the diversity and distribution patt of cyanobacteria and Microcystis in large,shallow,entropic lakes with significant spatial heterogeneity and long-term Microcystis bloom.Molecular methods based on denaturing gradient gel electrophoresis and clone library analysis were used.A similar heterogeneous distribution patt of cyanobacteria in both lakes was observed.Most parts of these two lakes with high trophic level were dominated by Microcystis.However,in the regions with low trophic levels as well as low concentrations of chlorophyll a,Synechococcus occupied a considerable percentage.Different morphospecies and genotypes dominated the bloom-forming Microcystis populations in these two lakes.Microcystis viridis and Microcystis novacekii were dominant in Lake Chaohu,whereas Microcystis flos-aquae was dominant in Lake Taihu.Only 2 of thel3 Microcystis operational taxonomic units were shared between these two lakes.Analysis of molecular variance based on 16S to 23S intal transcribed spacer sequences indicated the significant genetic differentiation of Microcystis between these two lakes (Fst =0.19,p ＜ 0.001).However,only 19.46％ of the genetic variability was explained by the population variation between lakes,whereas most (80.54％) of the genetic variability occurred within the lakes.Phylogenetic analysis revealed no phylogeographic structure of Microcystis population in these two lakes,as illustrated by their cosmopolitan nature.Our results revealed that spatial heterogeneity within lakes has more impact on the cyanobacterial diversity than geographical isolation in a local scale.