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In plants, flavonoids play roles not only in development, but also in responses to biotic and abiotic stresses. We analyzed the transcriptome data of NaCl-treated Reaumuria trigyna, a small, highly haloduric desert shrub, focusing on the flavonoid biosynthetic pathway. We identified 118 unigenes annotated as genes encoding enzymes related to flavonoid biosynthesis, 68 of which were differentially expressed under NaCl treatment (39 upregulated, 29 downregulated). Of the 118 annotated unigenes, 47 were annotated as members of families related to the flavonol biosynthetic pathway (e.g., F3H, FLS, and OMT). Of those 47 genes, about 70 % (32 unigenes) were upregulated under NaCl treatment. Experiments were conducted to monitor changes in gene expression and accumulation of total polyphenols, total flavonols, and antioxidant capacity under NaCl and ultraviolet-B (UV-B) radiation treatments. The expressions of genes related to the flavonol biosynthesis pathway (RtC4H, RtCHS, RtF3H3, RtFLS1, RtFLS2, RtF3’5’H, RtF3’H, RtOMT, and RtMYBF1) increased under NaCl and UV-B treatments. Treatments with NaCl and UV-B also increased the total flavonols content and antioxidant activity. The content of several flavonols including rutin, hyperoside, isorhamnetin-3-O-neohespeidoside, and myricetin increased in response to NaCl and UV-B stresses. Overall, our results show that the expression of genes related to flavonol biosynthesis as well as flavonol content increased in R. trigyna under NaCl and UV-B stresses.