Antioxidant enzyme activity, photosynthetic pigment content, and free malondialdehyde （MDA）, as well as flavonoid content and the key enzyme activity in the flavonoid pathway were determined in two desert shrubs, Caryopteris mongolica Bunge and Reaumuria soongorica （Pall.） Maxim. under drought stress. The free MDA content was enhanced during the experimental period, which may be an indicator of oxidative stress. Superoxide dismutase （SOD）, peroxidase （POD）, and ascorbate peroxidase （APX） activities in C. mongholica showed a significant increase during the experiment, but catalase （CAT） activity was slightly decreased. On the other hand, POD and APX activities showed a significant increase and SOD and CAT activity data had no significant changes in R. soongorica. APX, SOD, and CAT activities were higher in R. soongorica than in C. mongholica, but MDA content was lower, indicating that the lower values of MDA were attributed to higher activities of antioxidant enzyme in R. soongorica. Chlorophyll content decreased significantly in the two shrubs during the experiment, which indicated that there was a photoprotection mechanism through reducing light absorbance by decreasing pigments content. Caretonoids content increased in C. mongholica and decreased in R. soongorica. The ratio of Chla/Chlb decreased significantly but caretonoids/Chl revealed a significant increase in the two shrubs, which could be explained as no decrease of peripheral light-harvesting complexes and a higher tolerance to drought. Total flavonoid content and the activities of phenylalanine ammonialyase （PAL） and chalcone isomerase （CHI） showed different changes between C. mongholica and R. soongorica after treatment. These values decreased in R. soongorica and increased in C. mongholica except for PAL activity. However, anthocyanin content increased in the two shrubs, indicating that there was a different regulation response in the ftavonoid pathway in the two shrubs under drought stress, and anthocyanin should be an
