<p><i>Ammi majus</i> L. is a suitable source for linear, angular furanocoumarins, which have significant medicinal value. There is still a lack of extensive research on the genes involved in the biosynthesis of those valuable metabolites. For this purpose, transcriptome sequencing was performed on immature fruit and the resulting data was assembled as a de novo by Trinity software. Afterward, around seventy thousand transcripts were identified. Further analysis revealed the identification of thirty-eight genes involved in the biosynthetic pathways of MEP, MVA, linear and angular furanocoumarins, monoterpenoids, and sesquiterpenes. The content of psoralen, xanthotoxol, isopimpinellin, and pimpinellin was also measured in vegetative leaves, immature fruit, and fruiting leaves. Generally, the concentration of the metabolites was higher in immature fruit compared to other tissues. The expression of Amblyferon-8-dimethylallyl-transferase (U8DT), Amblyferon-6-dimethylallyl-transferase (U6DT), Psoralen synthase (PS), and Xanthotoxol-o-methyltransferase (XOM) were much higher in the immature fruit tissue than those in fruiting and vegetative leaves. The results showed that the expression of the U8DT gene in immature fruit increased 13.3-fold compared to vegetative leaves. The U6DT and PS genes in immature fruit tissue exhibited a 1.6-fold increase in expression compared to vegetative leaves, while the XOM gene showed a 1.5-fold increase in immature fruit compared to vegetative leaves. Integrated metabolome and transcriptome analysis indicated that these genes may serve crucial roles in furanocoumarins biosynthesis in <i>A. majus</i>. These findings can be a good prospect for further research in secondary metabolite production and metabolite engineering in this plant.</p> Graphical Abstract <p></p>