Isatis violascens Bunge is a spring ephemeral plant occurred in the sandy deserts of Junggar (or Dzungaria) Basin.It was suggested as a synonym of Isatis emarginata based on their morphology similarity.I.violascens has not been included in any molecular studies to date and its phylogenetic relationship is unknown.In present study,the nuclear ribosomal internal transcribed spacer(ITS) of I.violascens was sequenced.27 samples representing 18 Isatis species were analyzed using most parsimony,most likelihood and Bayesian method.Two well supported clades of Isatis were confirmed.I.violascens was closely related with I.emarginata and I.minima.From the evidence of similarities of morphology and low distance of ITS sequences,we provisionally agree with the merge of the two species and the reduction of I.violascens to synonym of I.emarginata.