| This paper constructed and analyzed RAPD and AFLP fingerprinting of new special cultivars 'Chunyu' and 'Hu No. 2' under protective cultured system, finding the unique RAPD and AFLP bands of' chunyu' and AFLP bands of' Hu No. 2' which will be useful in the property protection. At the same time, RAPD, ISSR and AFLP were used to be detected the genetic diversity in ten representative ecotype materials. The main results of this paper are as followers:1. Analysis of RAPD Fingerprints of Cucumber Cultivar 'Chunyu'26 primers stably amplified were selected from 300 random primers and were used to amplify the DNA of 21 cucumber accessions including newly breed cultivar 'Chunyu'.80 bands revealed polymorphism amomg the 173 amplified bands, amount to 46.24%, length scale of which was 100-1500bp. The unique 400 bp missing band with E13 primer in cultivar 'Chunyu'could be used as fingerprint for the protection of its intellectual property. The combination of different primers can distinguish all accessions. The accessions were classified into three groups at similarity coefficient 0.676 in UPGMA claster analysis using MEGA softerware, which has the same point with the ecotypic claster.2. AFLP Molecular Analysis of Genetic Difference between Cultivars in CucumberFive pairs of AFLP primers (E+TA/M+CTC, E+TC/M+CTA, E+TT/M+CTG, E+AG/M+CAT, E+AG/M+CAG) were selected from 32 pairs, which had equal bands, rich polymorphism and strong distinguished capability. Twenty-one bands showed polymorphism amomg the 282 amplified bands, the percentage of which was 7.45%. The genetic similarity and distance were 0.926 and 0.074 respectively, which showed the two cultivars were relative, while still had distinct difference, which can be distinguished in DNA level. This provided the evidence for identifying the cucumber cultivars with close relation and similar morphologic character. The key techniques of AFLP analysis system applied in cucumber were also discussed.3. Optimization of the ISSR-PCR System of Cucumber...
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