We report the first phylogenesis of 38 Sun/Air-Cured tobacco germplasms analyzed by Simple Sequence Repeat (SSR) Markers in this study. 30 primer pairs were randomly selected from a nearly total of 3000 tobacco SSR primers which were developed by our own. A total of 173 polymorphic alleles were amplified in 38 varieties using 30 SSR primers, and the number of alleles detected by each SSR primer ranged from 2 to 11, with an average of 5.77 alleles per markers. Genetic similarity coefficient (GS) among the 38 varieties ranged from 0.165 to 0.928, with an average of 0.546, which indicated the genetic variation of the 38 varieties was quite large and the genetic diversity was much abundant in Sun/Air-Cured tobacco varieties. The result of cluster analysis based on SSR markers showed that 38 varieties could be clustered into 2 groups: Sun/Air-Cured and TI tobacco groups, at a relative low level of GS=0.165. And the Sun/Air-Cured group was further classified into 4 subgroups, which was basically according with expected case. The study finally showed that SSR is a stable, reliable and valuable molecular marker system which was more efficient in generating accurate information on genetic background and relationship of tobacco, especially in Sun/Air-Cured germplasms.