Astragali Radix (AR), prepared from the roots of Astragalus membranaceus (FISCH. ex LINK) BUNGE or its variey, A. membranaceus (FISCH. ex LINK) BUNGE var. mongholicus (BUNGE) HSIAO., is one of the most used and valuable traditional Chinese medicines (TCMs). Historically, Hunyuan, Shanxi Province in China is the geo-authentic producing area of AR and crude AR from here called "geo-authentic." According to tradition, geo-authentic TCMs define both authenticity and quality. However, no scientific investigation has ever determined whether the superior quality of Hunyuan AR is due to the genetic characteristics or to the local environment. In our study, seeds of 30 AR samples representing the two varieties from different regions were cultivated in Hunyuan under the same conditions. A method, using ultra-performance liquid chromatography coupled with photodiode array detector and evaporative light scattering detectors, was developed to evaluate the quality through a simultaneous determination of four major isoflavonoids and four major saponins. The two AR varieties were successfully distinguished by principal component analysis while samples of the same species with different seeds origins could not be distinguished. A genetic study demonstrated that the internal transcribed spacer sequences of the nuclear ribosomal DNA in A. membranaceus var. mongholicus samples from different geographical regions were highly conservative. These results indicate that the content of active components in AR depends on the interaction of genotype and environment. At the varietal level, genetic properties appear to be more important for pharmaceutical quality than environmental factors, while on the intraspecific level environmental factors might be more important than genetic properties.