Both microwave-assisted extraction (MAE) and ultrasound-assisted extraction (UAE) have been widely applied in the extraction of a variety of biologically active compounds including carotenoids due to their lower pollution to environment, high extraction efficiency, lower cost, and shorter extraction time as compared to conventional extraction techniques. However, there are few reports on their effects on the stability of these compounds. In the present study, the stability of (all-E)-astaxanthin, one of the carotenoids, was examined under the action of both ultrasound and microwave. Results showed that microwave induced the isomerization of (all-E)-astaxanthin to its Z analogues, preferentially to (13Z)-astaxanthin as analyzed by HPLC coupled with diode array detection and LC-MS; and the percentage of the isomerization increased with increasing both treatment time and microwave power. In contrast to the microwave, the ultrasound degraded (all-E)-astaxanthin to unidentified colorless compound(s) as suggested by HPLC analysis and UV/vis measurements, and the degradation likewise increased as both treatment time and ultrasonic power increased. The results presented here emphasized that both MAE and UAE techniques should be carefully used in the extraction of unstable compounds such as (all-E)-astaxanthin.