Background Selenium hyperaccumulation in plants often involves the synthesis of non-proteinaceous methylated selenoamino acids serving for the elimination of excess selenium from plant metabolism to protect plant homeostasis. Methods Our study aimed at the identification of the main selenium species of the selenium hyperaccumulator plant Cardamine violifolia (Brassicaceae) that grows in the wild in the seleniferous region of Enshi, China. A sample of this plant (3.7 g Se kg-1 d.w.) was prepared with several extraction methods and the extracted selenium species were identified and quantified with by liquid chromatography mass spectrometry set-ups. Results The Cardamine violifolia sample did not contain in considerable amount any of the organic selenium species that are often formed in hyperaccumulator plants; the inorganic selenium content (mostly as elemental selenium) accounted only for less than 20% of total Se. The most abundant selenium compound, accounting for about 40% of total Se was proved to be selenolanthionine, a selenium species that has never been unambiguously identified before from any selenium containing sample. The identification process was completed with chemical synthesis too. The molar ratio of lanthionine:selenolanthionine in the water extract was ca. 1:8. Conclusions Finding selenolanthionine as the main organic selenium species in a plant possibly unearths a new way of selenium tolerance.