Background : Solanum nigrum Lin. is an annual herbaceous plant which belongs to the family Solanaceae as known the important medicinal herb and health-benefiting plant. Phytochemical investigation of whole plant reported that contain total alkaloids, steroid alkaloids, steroidal saponins, flavonoids, tannins, glycosides, proteins, carbohydrates, coumarins and phytosterols, and glycoproteins, exhibiting antitumor activity. Methods and Results : The accumulation of anthocyanin known as synthesis by flavonoid biosynthesis pathway is increased by AtPAP1 transcriptional factor. To identify the effect of AtPAP1 in S. nigrum, we generate AtPAP1-overexpressed S. nigrum and investigate total anthocyanin in these transgenic lines. The transgenic lines resulted in increasing the total anthocyanin amount compared with control line. Thus, the transgenic lines appeared purple colored leave as well as light purple in flower petal and dark purple in flower anther. To identify that AtPAP1 affects the genes profiling of anthocyanin biosynthetic pathway in S. nigrum, we harvested the AtPAP1-overexpressed S. nigrum transgenic lines and proceeded to qRT-PCR analysis. The result indicated that AtPAP1 gene highly induces in transgenic lines and the most upstream pathway genes of flavonoid such as SnPAL, SnC4H, Sn4CL, SnCHI and SnHCT are induced by AtPAP1 overexpression, excepting UGT75C1. According to these results, those functional genes may be regulated by AtPAP1 transcription factor. Thus, the purple color appearing in AtPAP1-overexpressed S. nigrum plants may be regulated by those genes. Conclusion : When AtPAP1 is overexpressing, the most genes in flavonoid pathway upregulate and activate resulting in accumulation of anthocyanin compound in leave and flower organs in S. nigrum. Ultimately, our data will be helpful for further research in S. nigrum molecular and physiology and better strategies for exploiting its phytochemical properties.