Abstract: Amplified fragment length Polymorphism (AFLP)was used to evaluate the genetic diversity of 27 accessions of gastrodia B1 elata from 5 provinces of china . A Total of 548 bands ranging in size from 100bp to 2500bp was generated from 16 primer combinations screened from 64 primer combinations and 428 of these bands showed polymorphism.The polymorphic ratio(PP) is up to 78% .Results showed that some genetics diversity existed among gastrodia B1 elata accessions from the different regions and AFLP can be used to investigate effectively genetic diversity of gastrodia B1 elata.The analysis of genetic variation indicated that the genetic distant among 27 accessions ranged form 0.54 to 0.018 ,with an average of 0.1904,which implied that the genetic discrepancy of gastrodia elata B1 from different sources was not high and the genetic diversity of gastrodia elata B1 was limted. However the genetic variance of gastrodia elata B1 accessions from Guizhou was more evident than that from other areas ，which indicated that there was abundant gene resource of gastrodia B1 elata in Guizhou province.Therefore, the accessions from Guizhou can become significant germplasm resources in the genetic improvement of gastrodia elata B1. The investigation on different forms of Gastrodia elata B1 from the same places using AFLP analysis illustrated that the variance of inter-specific level was morphologic variation.Whether the classficiation of Gastrodia elata B1 forms was correct still needed farther investigation.