Abstract: Sixteen poplar clones were used to analyse the genetic differences between Genomic-SSR and EST-SSR. The statistical results showed that the average number of alleles detected by Genomic-SSR was 4.1, Shannon was 1.064 6, heterozygosity was 0.442 7, expected heterozygosity was 0.552 3; while for the EST-SSR, the average number of alleles was 2.8, Shannon was 0.698 5, heterozygosity was 0.233 0, expected heterozygosity was 0.468 4. Cluster analysis indicated that the EST-SSR capacity of genotypes identification was more precise than Genomic-SSR. In a word, all these results reveal that the EST-SSR and Genomic-SSR have significant genetic differences in markers polymorphism and genotype identification, and that the differences would provide theoretical basis for the rational use of SSR marker in species diversity and other related research.