<jats:title>Abstract</jats:title><jats:p>This study sought to determine the primary components (isoquinoline alkaloids, diterpenoids and steroids) in crude extracts of the Chinese herb Jin‐Guo‐Lan, prepared from the roots of <jats:italic>Tinospora sagittata</jats:italic> and <jats:italic>T. capillipes</jats:italic>, by liquid chromatography/electrospray ionization multistage mass spectrometry coupled with diode‐array detection (LC‐DAD/ESI‐MS<jats:sup>n</jats:sup>). After separation on a reversed‐phase C<jats:sub>18</jats:sub> column using gradient elution, positive and negative ESI‐MS experiments were performed. In positive ion mode, the three types of compounds showed very different characteristic ions: strong [M]<jats:sup>+</jats:sup> or [M+H]<jats:sup>+</jats:sup> ions were observed for isoquinoline alkaloids; [M+NH<jats:sub>4</jats:sub>]<jats:sup>+</jats:sup> and/or [M+HCO<jats:sub>2</jats:sub>]<jats:sup>+</jats:sup> for diterpenoids; [M+HnH<jats:sub>2</jats:sub>O]<jats:sup>+</jats:sup> (n=1–3) for steroids. These adduct ions and/or fragments were used to deduce the mass and categories of known and unknown components in crude extracts, and their structures were further confirmed by ESI‐MS<jats:sup>n</jats:sup> in positive ion mode. Moreover, UV absorption peaks obtained from DAD provided useful functional group information to aid the MS<jats:sup>n</jats:sup>‐based identification. As a result, 11 compounds were unambiguously identified by comparing with standard compounds and 13 compounds were tentatively identified or deduced according to their MS<jats:sup>n</jats:sup> data. Two of these compounds (13‐hydroxycolumbamine and 13‐hydroxyjatrorrhizine) were found to be new compounds and another one (13‐hydroxypalmatine) was detected for the first time as a natural product. In addition, a [M·CH<jats:sub>3</jats:sub>H<jats:sub>2</jats:sub>O]<jats:sup><jats:bold>.</jats:bold>+</jats:sup> ion in MS<jats:sup>2</jats:sup> of [M]<jats:sup>+</jats:sup> after in‐source collision‐induced dissociation was used to differentiate positional isomers of protoberberine alkaloids, columbamine and jatrorrhizine. Although the roots of <jats:italic>T. sagittata</jats:italic> and <jats:italic>T. capillipes</jats:italic> contain almost identical compounds, the content of the compounds in them is dramatically different, suggesting the necessity for further comparison of the bioactivities of the two species. Copyright © 2006 John Wiley & Sons, Ltd.