A novel indole glucosinolate, 1,4-dimethoxyglucobrassicin (1,4-dimethoxyindol-3-ylmethylglucosinolate), was isolated as the desulfo derivative from roots of the P-type of Barbarea vulgaris ssp. arcuata, and its structure was determined by spectroscopy including 2D NMR spectroscopy. 4-Hydroxyglucobrassicin (4-hydroxyindol-3-ylmethylglucosinolate) was isolated as the desulfo derivative from green siliques (fruits) of Arabidopsis thaliana and identified by comparison of its (1)H NMR spectrum with the spectrum of the known desulfoglucosinolate from Brassica napus. The delayed elution of desulfo indole glucosinolates from the DEAE Sephadex column used in sample preparation was examined, and the diode-array UV spectra of desulfo indole glucosinolates were measured, to ensure a reliable determination of 1,4-dimethoxyglucobrassicin and 4-hydroxyglucobrassicin with the existing analysis method based on the HPLC of desulfoglucosinolates. 1,4-Dimethoxyglucobrassicin was not detected in 10 other Arabidopsis, Brassica, and Barbarea species, indicating an evolutionarily recent mutation in the indole glucosinolate biosynthesis in B. vulgaris ssp. arcuata type P.