A phytochemical study on the seeds of Peganum harmala led to the separation of 22 alkaloids, including quinazoline alkaloids (1-10), /3-carboline alkaloids (11-18), and others alkaloids (19-22). Their structures were identified by comprehensive spectroscopic analysis and comparison with literature data. Compounds 14 and 20-22 were first isolated from Zygophyllaceae family. Compounds 8 and 15 were firstly discovered as natural products. Moreover, the chemotaxonomic significance of the isolated alkaloids is discussed.