Bulbophyllum auricomum Lindl. is a commercially important, endangered orchid in Myanmar. Maintenance of genetic variation is considered essential for the long-term survival of a species. In the present study, DNA fingerprinting profile was used to evaluate the genomic variations among 20 randomly selected in vitro regenerated seed derived plants. A total of twelve random primers have generated 101 polymorphic loci (69% of total amplified loci). Genetic polymorphisms between 20 randomly selected in vitro regenerated plants and the donor plant were used to generate a genetic distance matrix based on Nei’s similarity coefficient. Genetic distances between the donor plant and culture regenerants were from 0.23 to 0.38, and 0.05 to 0.30 within 20 regenerants. Dendrogram constructed based on genetic distance matrix revealed two major sub-clusters accommodating all these 20 culture regenerants, while the donor plant appeared as an outgroup. Genomic variations developed among seed derived in vitro regenerated plants. The present findings indicate crosspollinating nature of the plant and presence of heterogeneous seed population. On the other hand, clonal propagation of in vitro raised plants maintained their clonal fidelity. It has been demonstrated that DNA fingerprinting profiles could be successfully employed to detect genomic variability, if any, at the early stages of shoot differentiation in this native endangered orchid. © Archana Sharma Foundation of Calcutta 2011.