Abstract: As a non-leguminous and nitrogen-fixing tree species, Alnus cremastogyne is also the most important endemic species of Alnus in China, which has important ecological functions. In this paper, the genetic differences of Genomic-SSR and EST-SSR markers in Alnus cremastogyne genome were analyzed. The results showed that the average number of alleles and the average number of effective alleles with EST-SSR were higher than those of genomic-SSR, while the average observed heterozygosity and average expected heterozygosity were higher than those of EST-SSR. Cluster analysis showed that there were differences between genomic-SSR and EST-SSR in small groups, which indicated that there were some differences between Genomic-SSR and EST-SSR in analyzing genetic diversity and genetic relationship to a certain extent, and more objective results could be obtained by combining the two marker methods.