In order to explore the applicability of capillary electrophoresis and polyacrylamide electrophoresis and compare their advantages and disadvantages, 8 sugar beet cultivation resources were used as materials, 8 SSR loci were selected. The polymorphism of each locus was detected by polyacrylamide gel electrophoresis silver staining and capillary electrophoresis. And then the results of the two methods were compared. Capillary electrophoresis fluorescence labeling method could accurately obtain the molecular size of DNA fragments. PAGE electrophoresis could only estimate the approximate molecular weight with the naked eye compared with Marker, but could not obtain the accurate molecular weight. The matching ratios of the two detection methods with the 8 pairs of primers were 75%, 87.5%, 50%, 75%, 25%, 100%, 37.5% and 50%, respectively. According to the results, there were great differences in data integration between the two detection platforms. The detection results were directly related to the factors like whether the primers were single copy, primer polymorphism and stability. The sequencing test results showed that when there were fewer samples, using PAGE electrophoresis to detect the polymorphism of SSR loci could not only save cost and time, but also ensure the accuracy of the test results.