Abstract: Four Betula alnoides strains in Yunnan Province were selected and the total genomic DNA was extracted with the modified CTAB method, by contrast with commercial strain, the relations of 4 B.alnoides strains′s genetic diversity, genetic distance and genetic clustering were studied. The result indicated that 4 pairs of specific primers have been screen out from 121 pair of primers by SSR molecular marker technique, and used for SSR-PCR amplification. 60 sites were amplified, and the percentage of polymorphic sites PPB=95.00%, Nei′s gene diversity index H=0.326 5, Shannon information index I=0.489 7, genetic differentiation coefficient between population G_st=0.211 4. The genetic diversity of all the B.alnoides samples was high, and the genetic variation was mainly in the strain. The genetic distance between strain1 and strain2 was the closest (D=0.089 1), strain3 and strain4 has the farthest(D=0.172 7). The cluster analysis of UPGAM showed that there were 3 categories, strain1 and strain2 were in one category, strain4 and commercial strain were in the second category, and strain3 in the third category.