Gastrodia elata Bl. is a rare and endangered traditional medicinal plant in China.The difference among germplasms is tiny in morphological characteristics, while is prominent in medical components, which results in its germplasm confusion in both cultivation and pharmacy. With the aim to construct DNA fingerprinting for G. elata germplasm, we used simple sequence repeat (SSR) molecular markers in this study to analyze the population genetic structure for G. elata with its 120 samples collected from 12 populations of its 3 forms (G. elata Bl. f.glauca S. Chow, G. elata Bl. f.elata, G. elata Bl. f. viridis Makino). As the results shows: (1) seven pairs of SSR primer were successfully used in the PCR amplification, and performed abundant polymorphism, the number of allele per primer pair (N_a) ranged from 5 to 7 with the average of 6.43, while the polymorphism information content (PIC) ranged from 0.626 2 to 0.823 5 with the average of 0.759 5. (2) Genetic diversity analysis of all samples of G. elata showed that the genetic diversity was high (species level: A=6.428 6, H=0.789 0, I=1.682 9; form level: A=2.666 6, H=0.523 9, I=0.812 3). (3) Analysis of molecular variance (AMOVA) analysis revealed strong genetic differentiation was happened among both populations and the forms (F_st=0.558 6, F_ct=0.381 8). (4) Cluster analysis showed that the populations of the same form clustered together firstly, 3 forms were separated completely. SSR fingerprinting had a good identification effect at the form level; 106 genotypes were detected from the 120 samples in total. The Simpson index (D) was 0.998, indicating the SSR fingerprinting has good ability of identification on the individual level. The study revealed the genetic background of G. elate, which provided scientific and technical basement for its conversation,germplasm selection and identification.