Surfactants can affect biological activities and pose serious threats to the aquatic ecosystem if discharged without proper treatment. Rhamnolipid is a biosurfactant with promising agricultural, industrial and biomedical applications. It is important to assess the risks posed by rhamnolipid before it is adopted for large scale use. In this study, toxicity of rhamnolipid was estimated with the effects of motility loss, membrane permeability, and cell lysis using a phagotrophic alga Ochromonas danica. O. danica is a sensitive algal species without a protective cell wall and it represents a group of phagotrophic flagellates ecologically important in the aquatic ecosystem. A common synthetic surfactant, sodium dodecyl sulfate (SDS), was used for comparison. Results suggested that rhamnolipid is significantly less biolytic than SDS and the effects required longer exposure. Lysis of O. danica cells by rhamnolipid was serious only at concentrations over its critical micelle concentration. Motility loss was, however, significantly more sensitive; about 75% loss after 20 min exposure to 50 mg/L rhamnolipid.