GbMYB1, a member of a new subgroup of the R2R3 MYB family of transcription factors, was cloned from a Ginkgo Biloba cDNA library with degenerate primers targeted to the highly conserved R2R3 MYB domain. This gene was preferentially expressed in the wood forming tissues, and corresponding protein was localized in the nucleus. Ectopic expression of GbMYB1 in Arabidopsis led to some change of phenomenon in transgenic plants, shorter root, delayed flowering time, reduced growth and probably enhanced lignin deposition in some xylem cells. Quantitative RT-PCR data showed that ectopic expression of GbMYB1 resulted in up-regulation of many genes encoding enzymes involved in lignin biosynthetic pathway and the PAL2 gene encoding the first enzyme in the general phenylpropanoid pathway. Together these results suggested that GbMYB1 might be involved in the control of phenylpropanoid metabolic pathway and lignin biosynthesis of Ginkgo biloba trees.