BackgroundDried roots of Sophora flavescens Aiton contain many phytochemicals that exhibit beneficial effects on human health. This study examined and compared the karyological, morphological and phytochemical characteristics of three S. flavescens populations collected from the Danda, Hualien and Yuli of Taiwan and a population collected from Gansu, China.ResultsKaryotypes of the four populations were similar, with a diploid number of 2n = 18. The Hualien population produced more roots but with less matrine and oxymatrine contents in its root tissue than others. However, only the root of Danda population had a measurable level of naringenin. The dried root of Yuli population had greater ferric reducing antioxidant power and trolox equivalent antioxidant capacity than that of the other populations.ConclusionsThus, the collected S. flavescens populations, particularly the population collected from Danda, have the potential to be used in breeding programs.Electronic supplementary materialThe online version of this article (doi:10.1186/1999-3110-55-5) contains supplementary material, which is available to authorized users.