Understanding the correlation between genetic diversity and species diversity in freshwater communities is important to elucidate the influences of local selective forces on the genetic diversity of local aquatic plant populations across different communities. This study employed amplified fragment length polymorphism (AFLP) to assess the genetic diversity of Potamogeton pectinatus L. populations between two sister-lakes with contrasting trophic levels, eutrophic and oligotrophic, in the Yunnan Plateau in southwest of China. The results showed high genetic differentiation between eutrophic lake and oligotrophic lake. The genetic distances between P. pectinatus populations were significantly correlated with the species evenness, but not with difference in species richness of aquatic plant communities. The results underpinned that genetic diversity at interpopulation levels and local species diversity in plant communities are positively correlated. In addition, our results also suggested that habitat types might play an important role in the genetic diversity of the P. pectinatus populations between these two lakes.