Both the primary and secondary metabolisms of higher plants are influenced by environmental conditions. Peganum harmala L. synthesise amazing diversity of secondary metabolites, such as alkaloids, volatile oils, triterpenes or sterols. We have no detailed information on genetic chemical contents and particularly the fatty acid contents of this plant species in Iran. Therefore, population-based fatty acid and alkaloid analyses were conducted in four geographical populations. Seeds fatty acid analysis revealed linoleic acid, oleic acid and palmitic acid were the main components in seeds oil. The highest fatty acid component was the linoleic acid in both mature and premature seeds of four studied populations. Low levels of 18:3/18:2 ratio in mature seeds (>0.01) in comparison to premature seeds (> 0.04) were found. Grouping of the populations by WARD clustering, separated mature seeds from premature seeds. CCA plot of P. harmala populations based on fatty acid contents, revealing the influence of geographical features on population differentiation. The main alkaloid contents in premature and mature seeds were harmine and harmaline. PCoA plots of the studied populations based on alkaloid contents for both premature and mature seeds separated the populations from each other.
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