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Fingerroot (Boesenbergia pandurata (Roxb.) Schlechter) is an important Southeast Asia especially Indonesian’s plant that has many pharmacological activities. This plant contains several secondary metabolites such as flavonoids and their prenylated derivates like panduratin A that can be produced trough tissue culture techniques. This study aimed to produce secondary metabolites mainly flavonoids in the fingerroot cell cultures and explain their biosynthetic relationship. Bud’s meristem of fingerroot were initiated to forming callus and shoot in appropriate medium and also induced to produce rhizomes in in vitro condition. Panduratin A content was determined using HPLC. The dominant secondary metabolites were isolated and characterized using, chemical reagents and spectroscopic methods. Panduratin A can be produced through callus and rhizomes formation of fingerroot. Other two secondary metabolites have been indentified as phytosterol and cardamonin with the content 285.85 ± 8.36 % and 316.35 ± 0.82 % respectively which were higher than the original plant. Panduratin A, phytosterol and cardamonin which are supposed to have pharmacological activities have been produced using cell culture of fingerroot Boesenbergia pandurata (Roxb.) Schlechter with higher level compared to the original plants.