BACKGROUND: Fucoxanthin is a carotenoid that exerts multiple beneficial effects on human health, including antioxidant, anti-cancer, anti-diabetic and anti-obesity activity. In this study, the partition behavior of fucoxanthin in aqueous two-phase systems (ATPS) composed of ethanol and potassium phosphate was evaluated. This evaluation was performed 'en route' to establishing an ATPS extraction system for the recovery of fucoxanthin from microalgae cultures. System parameters including tie-line length (TLL), volume ratio (V-R) and product concentration were studied using model (purified fucoxanthin) and complex systems (microalgae extracts). RESULTS: ATPS comprising high TLL (70% w/w) and high V-R (>1) provided the best recovery of fucoxanthin in model systems. For complex systems, the best results were observed in systems with TLL 50% w/w and V-R = 1 for Phaeodactylum tricornutum methanolic extracts (95.36% recovery and 66.01% purity), and systems with TLL 60% w/w and V-R = 3 for Isochrysis galbana methanolic extracts (89.18% recovery and 78.74% purity). CONCLUSION: the findings suggest that the nature of sample solution, the hydrophobicity of the system, and the salting out effect have significant impacts on fucoxanthin partition. (C) 2014 Society of Chemical Industry