A phytochemical study on the methanol extracts from the seeds of Peganum harmala L. led to a new quizonaline alkaloid (S)-vasicinone-1-O-β-d-glucopyranoside (1) and four known ones, (R)-vasicinone-1-O-β-d-glucopyranoside (2), (S)-vasicinone (3), vasicine (4), and deoxyvasicinone (5). Their structures were elucidated by spectroscopic analysis including IR, HR-ESI-MS, 1D and 2D NMR, and specific rotation as well as by comparison of the data with those in the literature. All of the alkaloids were screened for antiproliferative activity against human gastric cancer cells MCG-803 with MTT method. Compounds 1 and 3 exhibited moderate inhibitory activity.