- We investigated a novel method for the selective separation of β‐carotene isomers from a freeze‐dried powder of the algae Dunaliella bardawil using supercritical fluid extraction. The separation method relies on the different dissolution rate of the 9Z and all‐E isomers of β‐carotene in SC‐CO2. At first, the equilibrium solubility of the two isomers in SC‐CO2 was determined at the extraction conditions of 44.8 MPa and 40°C. The solubility of the 9Z isomer was found to be nearly 4 times higher than that of the all‐E isomer (1.92 × 10−5 g all‐E isomer/g CO2 compared to 7.64 × 10−5 g 9Z isomer/g CO2). When supercritical fluid extraction was applied to a carotenoid concentrate from the algae (29 wt% β‐carotene) or a freeze‐dried powder of the algae (3.1% β‐carotene), a selective separation of the 9Z/all‐E isomers of β‐carotene was obtained. Thirty‐nine percent recovery of β‐carotene with 80% purity of 9Z isomer was achieved at the initial stages of extraction (40 mL CO2). The extraction rate of β‐carotene from the freeze‐dried algae powder was slower than that from the carotenoid concentrate, resulting in a reduction in the recovery and purity of the 9Z isomer. This indicates that even at the initial stage of the extraction the internal mass resistance is significant. Isomer purity and recovery could be enhanced upon grinding of the algae powder. © 2002 Wiley Periodicals, Inc. Biotechnol Bioeng 80: 169–174, 2002.