Abstract: Based on the ISSR molecular markers, agenetic comparison among 29 Oncidium germplasms was established.The 10 ISSR primers produced 144 DNA bands, averaging 14.4DNA bands per primer, and of which124 (86.11%) were polymorphic.The genetic similarity coefficients of the germplasms ranged from 0.34 to 0.91.At the similarity coefficient of 0.56, the 29 germplasm accessions were classified into 3groups.The clustering results were basically consistent with the traditional classification, which is closely correlated to the flower phenotype of germplasm resources.The result obtained from this study seemed to preliminarily validate the application of ISSR molecular markers for genetic analysis on Oncidium.