The application potential of duckweed (Lemna japonica 0234) and water hyacinth (Eichhornia crassipes) were compared in two pilot-scale wastewater treatment systems for more than one year. The results indicated duckweed had the same total nitrogen (TN) recovery rate as water hyacinth (0.4 g/m(2)/d) and a slightly lower total phosphorus (TP) recovery rate (approximately 0.1 g/m(2)/d) even though its biomass production was half that of water hyacinth. The higher content of crude protein (33.34%), amino acids (25.80%), starch (40.19%), phosphorus (1.24%), flavonoids (2.91%) and lower fiber content provided duckweed with more advantages in resource utilization. Additionally, microbial community discovered by 454 pyrosequencing indicated that less nitrifying bacteria and more nitrogen-fixing bacteria in rhizosphere of duckweed provided it with higher nitrogen recovery efficiency (60%) than water hyacinth (47%). Under the presented condition, duckweed has more application advantages than water hyacinth because it more effectively converted the wastewater nutrients into valuable biomass. (c) 2014 Elsevier Ltd. All rights reserved.