Abstract: The aim is to select the SCoT primer that suitable for the genetic diversity analysis of beet varieties. In this study, eight beet varieties from different countries were used as materials, and 80 SCoT primers were amplified. The optimal reaction system of SCoT-PCR was used in this study, it included 2.0 μL of 10×PCR buffer (Mg2+), 10 ng of template DNA, 0.5 U ofTaq DNA, 2 μL of 10 μmol/L primers and 0.1 μL of dNTPs (2.5 mmol/L each). As a result, 20 primers with high level of polymorphism were selected from 80 primers. In the 20 primers, some one amplified 16 polymorphic bands at most, and some one amplified 2 polymorphic bands at least. The total bands were 155, including 134 polymorphic bands, with a polymorphism rate of 86.5%. Through the validation of the core primer, the 20 core primers selected are suitable for the fingerprint construction of beet.