Abstract: The traditional way to extract DNA from pepper is using CTAB method. Now, the CTAB method could not meet the need for massive molecular biology work, in order to solve the problem, we testified alkalin-heating method in pepper DNA extraction. A SSR molecular marker that was recently identified from a new pepper variety was used as examining approach for checking whether the Alkalin-heating method can provide qualified DNA satisfying experimental needs. The results showed that different tissues should be used according to different experimental purposes. Roots of germinated seeds were needed when dealing with seed-purity-identifying. Young leaves of mature plants were needed when dealing with plant genetic screening. These plant materials were then put into PCR tubes. After adding 80 μL 0.2 mol/L NaOH solution, the tubes were treated under 100℃ for 30 mins in PCR amplifier. Then 40 μL Tris-HCl buffer was used to adjust pH value to a range between 7 and 8. Then a good experimental result could be retrieved using the DNA solution as template. In conclusion, it is confirmed that, comparing with other time and labor consuming methods, the Alkalin-heating method would be a more suitable way to solve the problem of high throughput genetic identification in pepper.