Dendrobium nobile is an important medicinal orchid having profound importance in traditional herbal
drug preparations and pharmacopeias worldwide. Due to various anthropogenic pressures the natural
populations of this important orchid species are presently facing threats of extinction. In the present
study, genetic and chemical diversity existing amongst 6 natural populations of D. nobile were assessed
using molecular markers, and the influence of genetic factors on its phytochemical activity especially
antioxidant potential was determined. Molecular fingerprinting of the orchid taxa was performed using
ISSR and DAMD markers along with the estimation of total phenolics, flavonoids and alkaloid contents.
Antioxidant activity was also measured using DPPH and FRAP assays which cumulatively revealed a significant
level of variability across the sampled populations. The representatives from Sikkim in Northeast
India revealed higher phytochemical activity whereas those from Mizoram showed lesser activity.
Analysis of molecular variance (AMOVA) revealed that variation amongst the populations was significantly
higher than within the populations. The data generated by UPGMA and Bayesian analytical models
were compared in order to estimate the genetic relationships amongst the D. nobile germplasm sampled
from different geographical areas of Northeast India. Interestingly, identical grouping patterns were
exhibited by both the approaches. The results of the present study detected a high degree of existing
genetic and phytochemical variation amongst the populations in relation to bioclimatic and geographic
locations of populations. Our results strongly establish that the cumulative marker approach could be
the best suited for assessing the genetic relationships with high accuracy amongst distinct D. nobile
accessions.