Artemisia martjanovii Krasch is a rare representative of the genus Artemisia in Siberia and the Far East. The phytochemical composition of this endangered species is essential for its potential use in medicine. We used tandem mass spectrometry and HPLC-MS/MS methods to describe the metabolome from the stem and leaf extracts of A. martjanovii from Yakutia. The metabolome profile analysis of A. martjanovii grown in the Botanical Garden of the North-Eastern Federal University, Yakutsk, Russia, and the wild A. martjanovii from Khangalassky district, Republic of Sakha (Yakutia) differed significantly both in the polyphenol composition and other compound classes. In total, we identified 104 bioactive constituents from stem and leaf extracts, 56 compounds from the polyphenol group, and 48 from other compound classes. Twenty-seven compounds classified as polyphenol groups, i.e., flavones apigenin, trihydroxy(iso)flavone, salvigenin, cirsiliol, cirsilineol, nevadensin, syringetin, gardenin B, thymonin, and chrysoeriol C-hexoside; flavonols: taxifolin, tetrahydroxy-dimethoxyflavone-hexoside, etc.; and 26 compounds from other classes are being reported for the first time in the genus Artemisia L.