India is endowed with a rich diversity of medicinal plants. These plants form the backbone of the traditional systems of medicine, and many medications have been semi-synthesized from lead compounds isolated from these plants. This rich natural resource, however, is disappearing rapidly due to various factors. Therefore, its conservation and management are of utmost importance. For planning effective conservation and breeding strategies, it is essential to have a thorough understanding of a species’ genetic makeup and diversity across different populations. It is a well-established fact that gene flow among populations and the percentage of polymorphism are key factors ensuring the survival of a species. There are very few studies on cytogenetic diversity and its correlation with phytochemicals at inter- or intraspecific levels in medicinal plants. This review provides a brief account of various cytogenetic approaches, including DNA markers, to assess the cytogenetic character and genetic diversity of some endangered medicinal plants. This approach may enable the identification of highly valuable genotypes in medicinal plant populations that should be prioritized for conservation.