The new alkaloid (2S,3S)-4-(5,6-dimethylpyrazin-2-yl)butane-1,2,3-triol (1) and 13 known alkaloids were isolated from the MeOH extract of fruit of Capparis spinosa L. The chemical structures of the isolated compounds were established by complex analysis using high-resolution mass spectrometry, UV and NMR (1D and 2D) spectroscopy, and electronic circular dichroism (ECD). The absolute configuration of the new compound was determined by comparing calculated and experimental ECD spectra.