Radix Polygalae, roots of Polygala tenuifolia or of Polygala sibirica, is a Chinese herbal medicine commonly used to prevent dementia. Reliable chemical markers for quality assurance of this herb are missing. Here, a high performance liquid chromatography method coupled with diode array detection was developed to simultaneously determine nine different phenols in Radix Polygalae, including sibiricose A(5), sibiricose A(6), glomeratose A, tenuifoliside A, glomeratose D, 3',6-di-O-sinapoyl sucrose ester, mangiferin, polygalaxanthone III, and polygalaxanthone XI. By using two different detection wavelengths in the HPLC analysis, the developed method was able to determine the phenols with excellent resolution, precision, and recovery. This established method was therefore applied to determine the amounts of phenols in thirty-two samples from different cultivation regions and harvest seasons in China, and significant variations were revealed. The amounts of phenols in the roots of P. tenuifolia collected in Shanxi and Shannxi Provinces were markedly higher than in roots collected from other Provinces. Moreover, the samples harvested in the spring contained higher contents of phenols than those collected in other seasons.