Peganum genus is rich with its high phytochemical and botanical variability. Peganum species have been used as a sedative, antitumor, analgesic and antidepressant. This paper aims to study the molecular diversity of Peganum genus and to shed more light on the structure-activity relationship of the alkaloids isolated from Peganum genus. All Peganum alkaloids were grouped according to their structural properties. A chemoinformatic approach (SwissTargetPrediction) was used to determine the molecular targets of these alkaloids. To analyze and visualize the results, R software was used to generate hierarchical clustering heatmaps. The results of this study can help researchers to better understand the structure-activity relationship of Peganum alkaloids and how substitution can affect the biological activity of those alkaloids.