BACKGROUND: Species of the Apiaceae family produce furanocoumarins-photosensitizing substances widely used in pharmacology. Among them, certain species of the genus Heracleum, commonly known as "giant hogweeds", are particularly renowned for their photosensitizing properties. While the metabolic composition of these plants has been studied extensively, their genomics remains largely unexplored, as does the biosynthesis of furanocoumarins within the genus. The reasons behind the increased photosensitivity of giant hogweeds compared to other Heracleum species remain unclear. RESULTS: A comparison of the genomic features and furanocoumarin content of the aboveground organs in two Heracleum species was carried out: H. sosnowskyi, a giant hogweed with strong photosensitizing activity, and H. sibiricum, a non-invasive and "harmless" species. Both species produce all known angular and linear compounds of the furanocoumarin synthesis pathway (from umbelliferone to isopimpinellin). The genomes of both species possess homologues of genes involved in the biosynthesis of both angular and linear furanocoumarins. However, the two species differ significantly in the quantity of those compounds. H. sibiricum synthesizes angular furanocoumarins in a much lower level, probably due to lack of the gene for umbelliferon-8-dimetylallyl transferase enzyme. H. sosnowskyi accumulates significantly higher level of xanthotoxin. Interpopulation differences were observed in both the compound content and the expression level of biosynthetic genes. CONCLUSION: This study represents the first comparative analysis of genomic and metabolic data for closely related Heracleum species in relation to furanocoumarin biosynthesis.