Although resveratrol-forming stilbene synthase (STS) genes have been well characterized in many plant species, there are only a few descriptions about STS genes from Polygonum cuspidatum Sieb. et Zucc, an important medicinal crop in Asian countries. To evaluate the biological functions of a Polygonum cuspidatum resveratrol synthase gene (PcRS), the PcRS gene was expressed in Arabidopsis under the control of Cauliflower mosaic virus (CaMV) 35S promoter. Integration and expression of transgene in the plant genome of Arabidopsis was confirmed by Southern blot and Northern blot analyses. Transgenic plants accumulated a new compound in both the leaves and seeds, which was identified as trans-piceid by high-pressure liquid chromatography (HPLC) and electrospray mass spectrometry (HPLC-ESI-MS). Overexpression of PcRS in transgenic Arabidopsis caused restriction of Colletotrichum higginsianum colonization by inhibition of spore production, resulting in enhanced resistance against C. higginsianum. So, the PcRS gene could be deployed in other crop plants to significantly enhance resistance to fungal pathogens and improve the nutritional quality. In addition, altered seed coat pigmentation and significant reduction in anthocyanin levels were observed in transgenic Arabidopsis, while the expression of endogenous chalcone synthase (CHS) gene was not down-regulated. These results suggest that additional STS activities cause a lack of precursors for CHS which leads to the disturbance of the subsequent flavonoid biosynthesis steps in Arabidopsis.