The dynamic changes of bacterial community in two eutrophic areas including Guanqiao Lake and Sea World,referred to as H and L,of Donghu Lake in spring and summer were studied with highthroughput sequencing. The results showed that the bacterial community structures in H and L areas were similar.Actinobacteria were dominated in these area,following by Cyanobacteria and Proteobacteria. The relative bacterial abundance varied with time in both areas tested. A large fluctuation was observed in H area that Cyanobacteria (10.2%-33.7%) and Actinobacteria (15.4%-53.1%) abundance varied with significantly negative correlation,while bacteria were relatively stable in L area at the phylum level. The abundance of several classes including Actinobacteria,Synechococcophycideae,Oscillatoriophycideae and Chloroplast in H area,and the Oscillatoriophycideae and Chloroplast in L area fluctuated greatly. The diversity index of L area was higher than that of H area. Results of RDA analyses showed that pH,water temperature and dissolved oxygen were significantly negatively correlated with bacterial community in both areas,while N/P and TP were strongly positively correlated with bacterial community of H and L areas.