Curcuma caesia Roxb. belonging to Zingiberaceae family is a rhizomatous perennial herb consisting of bluish black rhizome and having vast medicinal and pharmaceutical applications. It is considered as an endangered medicinal plant and native to India. The aim of this study is to assess the molecular diversity among the high rhizome essential oil yielding lines of C. caesia (> 1.5% w/w). The molecular diversity analysis was done by using 45 simple sequence repeat markers amongst the 78 high essential oil yielding lines of C. caesia. The overall percentage of polymorphism amongst the lines was found to be 53%. AMOVA analysis showed 20% and 80% variations among and within the population respectively. Dendrogram constructed using Unweighted Pair Group with Arithmetic Mean (UPGMA) for those high essential oil yielding lines sorted into five major clusters according to their different geographical locations. These five clusters were confirmed using principle component analysis (PCA), based on the Jaccard’s similarity coefficient. The results revealed that these microsatellite markers could be used as successful tool to differentiate the genetic makeup of the crop. Molecular diversity of C. caesia has not been studied till now. So, this is the first scientific report on molecular diversity analysis which may help in the further crop improvement programme and germplasm conservation also.