Abstract: 【 Objective 】 In the present study, the problems of gel background was too dark, band smear, the gel was distorted and DNA bands were bent in silver staining PAGE experiments were summarized and the method was optimized. 【 Method 】Genomic DNA of Brassica napus L. was employed as material, the reagent dosage and experimental conditions of PAGE electrophoresis and silver staining technique were adjusted to obtain the best effects. 【 Result 】Results showed that the staining effects were interfered by different factors, e.g. methanol concentration, voltage stability, electrophoresis temperature, bubbles trapped in gel and other issues. When methanol concentration was too high (1.25%), the gel background was too dark although staining in short time; if it was too low (0.001 25%), gel background was light but DNA bands were light too, and much longer time was needed to complete staining; unstable voltage could result in bands smear; when the electrophoresis temperature was too high, the gel was distorted and DNA bands were bent; bubbles in gel could disturb the shape of DNA bands. However, there was no significant difference in staining effect by adjusting NaOH concentration from 0.875% to 1.375%.【 Conclusion 】A modified silver staining PAGE method was concluded, which was improved as: 4 mL methanol (1%), stable voltage, electrophoresis in ice bath, and driving all bubbles in time in experimental system, and then a clear background with smooth, distinct bands could be obtained.