Camptothecin is a plant-derived alkaloid and important precursor of clinically used anti-tumor drugs, but little is known about regulatory mechanism of camptothecin production in plants. We show here that a MYB transcription factor, OpMYB1, isolated from Ophiorrhiza pumila is a regulator of camptothecin biosynthesis. OpMYB1 has an EAR-like motif and exhibits a transcriptional repression activity in an in vivo assay using Arabidopsis thaliana leaves. Overexpression of OpMYB1 in hairy roots of O. pumila resulted in reduced production of camptothecin and reduced expression of OpTDC encoding triptophane decarboxylase catalyzing the earliest step in camptothecin biosynthesis. From the deep transcriptome analysis, GO enrichment in secondary (specialized) metabolisms, especially in phenylpropanoid pathway was observed in the hairy roots over-expressing OpMYB1. Furthuremore, gene suppression by OpMYB1 was revealed in biosynthetic pathways of seco-iridoids, monoterpene indole alkaloids, anthraquinone and chlorogenic acid. These results suggested that OpMYB1 is a negative regulator to fine-tune the general specialized metabolisms in O. pumila.