For exploring the seasonal succession of planktonic diatom in shallow eutrophic lakes, two small shallow lakes—LakeQianhu and Lake Yueya in Nanjing were chosen and monitored monthly in 2006. We discussed the relationship between the diatomdensity, diatom assemblages and environmental factors by the analyses of CCA. The results showed the obvious seasonal successionsof diatom assemblages in the two lakes. Cyclostephanos was the dominant species in winter, representing the cool eutrophic diatomassemblage; while the assemblage changed into Cyclotella atoms and C. meneghiniana dominant in summer and autumn whichrepresented warm and eutrophic assemblage. CCA analysis using the monthly data indicated that temperature did not only control thebiomass of diatom, but also affected the seasonal succession of diatom assemblages. The increasing diatom biomass in spring had alittle contribution to primary production. When the level of eutrophication was higher, the temperature plays more important role ininfluencing the planktonic diatom.