Three new indole alkaloid glycosides were obtained from the roots of Isatis indigotica (I. indigotica). Compounds 1a and 1b were determined to be a pair of epimers with an unusual 1-[6-(1H-indole-3-yl)-2H-1,2,4-thiadiazin-3-yl]but-3-en-2-ol skeleton by chiral-phase chromatography and electronic circular dichroism (ECD) data analysis and their putative biosynthetic pathways were proposed. Compound 2 possesses an uncommon 5-(1H-indol-3-yl)pyrrolidin-2-one skeleton. Their nitric oxide (NO) inhibitory effects were tested in LPS-stimulated RAW 264.7 cells, however, none of them exhibited inhibitory activities. © 2020 Phytochemical Society of Europe