Abstract: In order to expedite the process of tobacco genetic analysis by using automatic and intelligent equipment, the capillary electrophoresis with fluorescent detection technique was applied to tobacco SSR analysis. Nine tobacco materials were analyzed by the capillary electrophoresis with fluorescent detection technique and the polyacrylamide gel electrophoresis technique. In the same materials and the same set of SSR primer, the detection efficiency of the two systems was compared, and the fluorescent detection technical system was established and optimized in tobacco SSR analysis. The results showed that the fluorescent detection technique overcame the shortage of silver staining and had merits of simple, reliable and high-throughput. The strategy for building low cost and high throughput multiple PCR system in microsatellite genotyping was also discussed.