Root exudates play an important role in rhizosphere interactions between plants and microorganisms. However, collection of chemicals from plant root system is difficult due to their low concentrations and high level of contaminants in growth media. The continuous collection method has been described in several terrestrial plants over the past 30 years (Tang and Young, 1982; Kong et al., 2004). Here, we describe a protocol for the collection of sterile root exudate from a floating aquatic plant, duckweed.