Duckweed is a group of aquatic plants with the potential of wastewater remediation and fast accumulation of biomass. The accumulated biomass, rich in cellulose, starch and protein, can be used for biofuel, bio-fertilizer, animal feed and human food. Characterization of natural biodiversity of duckweed species is essential for the germplasm preservation and various practical applications. We have collected samples of duckweed in eastern China and characterized species biodiversity by genotyping, using chloroplast (atpF-atpH and psbK-psbI spacers). Spirodela polyrhiza was revealed as a clear dominant duckweed species in all locations of the area. Other duckweed species were identified as Landoltia punctata, Lemna aequinoctialis and Lemna turionifera. Selected isolates of these four species were used in the experiments to estimate their potential in removing nitrogen and phosphorus nutrients from municipal and industrial wastewater sampled at the local sewage plants. Duckweed was able to reduce the concentration of nitrogen up to 98% and phosphorus up to 96%. The presented data demonstrates high efficiency of the local duckweed isolates for bioremediation of different types of wastewater and the great potential of duckweed for wastewater treatment when incorporated into the purification chain.