The reproducibility in migration time is essential in the use of capillary electrophoresis to identify components in a complex sample or compare constituent differences for different botanical drug samples. A powerful one-marker technology for correcting migration time was proposed in this paper. This technology is practically simple compared with the multi-marker technologies developed in literature, due to only one marker required. Paeoniae Radix which is a crude drug used in many traditional prescriptions in China and Japan was selected as an example to verify the effectiveness of the powerful one-marker technology in analyzing complex botanical samples. Relative standard deviations in migration times treated with the powerful one-marker technology were below 0.5% for Paeoniae Radix analyzed during three different days. The technology was successfully applied to classify Paeoniae Radix from nine different growing regions. Based on their corrected electropherograms, Paeoniae Radix was classified into three groups which were in agreement with their real origins.