Abstract: To amplify the SSR/InDel labeled products with clear and less nonspecific bands, twelve different genotype beet cultivars from six countries were selected. The products were amplified using SSR markers, InDel markers and three PCR procedures, including touch-down PCR, gradient PCR, and conventional fixed annealing temperature PCR. By comparing the polymorphism, stability, and clarity of the amplification product, a PCR reaction program suitable for both molecular markers was selected. The results show that the touch- down PCR method can successfully amplify the sample products with clear bands and stable amplification effect, without invalid product through a single reaction. Gradient PCR amplification results are unstable, there are non-specific bands and diffuse phenomenon is serious. The fixed annealing temperature PCR has different amplification results due to different primers, and accompanied by diffusion phenomenon. The specificity and stability of touch-down PCR amplification products are higher than that of gradient PCR and fixed annealing temperature PCR, meanwhile the process of groping the optimal annealing temperature is omitted compared with gradient PCR method. Therefore, touch- down PCR procedure is recommended for sugar beet SSR and InDel molecular markers