Abstract: From April 2009 to September 2011, we conducted a survey of phytoplankton diversity in the lakes Hasuhai and the Wuliangsuhai of Inner Mongolia, and also analysed the relationship between phytoplankton diversity and environmental factors. Using the Shannon-Weaver diversity index, the Margalef abundance, Pielou evenness calculated and SAS9.0 Software to analyse data.The results showed that Hasuhai phytoplankton evenness index showed a high degree of positive correlation with the ion coefficient, calcium and magnesium ratio; abundance index, the diversity index showed a negative correlation between them and the ion coefficient, alkalinity, total hardness. Wuliangsuhai phytoplankton evenness, diversity index and the abundance index showed a high degree of correlation with the ion coefficient, calcium and magnesium ratio and total hardness.