The Zingiber species comprises rhizomatous plants with special significance due to their multiple uses. Previously, we reported the additional use and suitability of primer pairs of rice microsatellite markers as RAPDs for diversity assessment in representative accessions of diverse taxa in the family Zingiberaceae. The current study aimed to investigate the genetic structure of Z. officinale at a genebank, small-scale subsistent farms and commercial markets, and the genetic relationships of three Zingiber species. A difference among accessions at the inter-specific level was observed and amplification of species-specific bands led to high polymorphism. Genetic variability in Z. officinale was exhibited by the three collection sources; however, some of the accessions from each source tended to cluster. AMOVA also displayed significant divergence among the three collection sources and explained most of the variance (87%) within the collection sources. In general, small-scale local farms displayed higher genetic variability in Z. officinale compared to those from the genebank and markets. Comparative assessment displayed high allelic diversity in ginger from Myanmar as compared to other Asian countries. Genetic resources of Zingiber species, particularly available on farms, can be a useful source to capture and utilize diversity for conservation as well as further improvement in gingers.