Abstract: Using 16 pairs of sugar beet SSR primers to amplify 12 different sugar beet varieties, 8% nondenaturant polyacrylamide gel electrophoresis, 3% Metaphor agarose electrophoresis and 3% agarose gel electrophoresis were adopted to test the products of SSR amplification respectively and the differences between the test results were compared. The results demonstrated that: the resolution capacity of 8% non-denaturant polyacrylamide gel on the difference in tiny bands was much higher than that of the 3% Metaphor agarose and the 3% agarose gel; the resolution ratio of Metaphor agarose was higher than that of the agarose gel. However, for primers with fewer bands, the 3 gels showed no difference; for primers with more bands, if the bands were concentrated, the 3 detection methods would produce significant difference; if the bands were scattered, the 3 gels would only present small difference. Since Metaphor agarose has higher prices, softer gel (harder to handle) and lower resolution ratio than polyacrylamide gel, it is not recommended. 8% polyacrylamide gel is suitable for fingerprint construction and genetic diversity analysis while agarose gel is applicable to identifying the purity of variety.