Bletilla striata Rchb. is an endangered plant with important medicinal values. It has many adulterants, while its wild resources was exhausted. In this study, 48 individuals of B.striata sampled from 16 populations, and 4 individuals from its each 3 relatives, including B. ochracea, B. formosana and B. sinensis, were analyzed with SSR markers aiming to reveal their genetic diversity and relationship, to construct their SSR fingerprinting. The results showed that: (1) 20 pairs of primer performed high polymorphism, the alleles ranged from 4 to 9 with summary 127 and average of 6.35 per primer, all of 20 primer were proved amplifiable in 4 species; (2) 7 pairs of primers, BJSSR01, BJSSR14, BJSSR15, BJSSR16, BJSSR18, BJSSR19 and BJSSR22, which performed higher polymorphism, higher polymorphism information content (PIC), were used to build the SSR fingerprints of B. striata and its adulterants.(3) The study revealed that the genetic diversity of B. striata was high (N_a = 6.35, I=1.429 1, H=0.706 8), genetic differentiation was prominent among species (G_st=0.44), and the gene flow among species was limited (N_m=0.475 3). (4) 4 major groups were generated from 60 accessions tested by UPGMA clustering analyses. Samples from same species were cluster together firstly, which is matched with their morphological taxonomy. Significant differences were revealed not only among the species, but also among the germplasms from different regions. Those with shorter geographic distance performed a tighter genetic relationship. The selection and protection of the excellent varieties of B.striata were also discussed.