Abstract: To investigate the effects of different detection methods on sugar beet ISSR primer polymorphism and their advantages and disadvantages, two kinds of detection methods, non-denaturing polyacrylamide gel electrophoresis and agarose gel electrophoresis were used to detect the amplification effect of sugar beet ISSR primers. 12 different varieties of sugar beet and 10 ISSR primers were used to amplify the production which were detected respectively by 6% non- denaturing polyacrylamide gel electrophoresis, 1% agarose gel electrophoresis and 2% agarose gel electrophoresis to separate the production of ISSR- PCR. The results showed that the number of polymorphic fragments or total bands detected by 6% non- denaturing polyacrylamide gel electrophoresis was more than that of agarose gel electrophoresis, and they were cleaner and more legible. However, the total bands on 2% agarose gel electrophoresis were more than or equal to that on 1% agarose gel electrophoresis. Thus, when we conduct QTL mapping, construct fingerprinting and analyze genetic diversity with ISSR primers, 6% non-denaturing polyacrylamide gel electrophoresis is recommended. While, for seed purity identification and the sequencing of ISSR amplification production, 2% agarose gel electrophoresis is more appropriate.