Abstract: To analyze the genetic diversities and structures of Sassafras tsumu and to explore their changing patterns at five different altitudes, Bioptic Qsep 100 DNA fragment analyzer combined with 13 SSR primers was applied. The results showed that S. tsumu in Tianmushan Mountain had a relatively high genetic diversity, with the expected heterozygosity (H_e) and observed heterozygosity (H_o) being 0.84 and 0.61, respectively. According to Shannon index (I), the diversity of S. tsumu at middle altitude (500-800 m) was higher than that at low (200 m) and high altitudes (1100-1400 m). The coefficient of genetic differentiation and AMOVA results indicated that the genetic variation of S. tsumu was mainly distributed within populations. UPGMA cluster analysis and STRUCTURE analysis showed that S. tsumu populations at the middle and lower altitudes were similar, but different from that at higher altitude. The differences in genetic distance of S. tsumu populations at middle and low altitudes revealed that human disturbance posed a negative effect on the diversity, whereas, natural reserve played a significant positive role in protecting species diversity.