Medicinal plants are an important component of global biodiversity, as they play a significant role in public health and cultural practices and generate substantial income for producing countries. It is estimated that over 50,000 plant species possess medicinal properties closely linked to their genetic diversity. Genetic variation present in medicinal plants is often considered a key factor in determining species or population resilience to environmental change and their phytochemical content, such as terpenoids, alkaloids, and phenolics. In many countries, the production of herbal and modern medicines still relies on wild populations of medicinal plants. At the same time, most wild medicinal plant species remain inadequately explored for their genetic and phytochemical properties. Medicinal plants, particularly the wild populations, are now facing threats from habitat degradation, overharvesting, and climate change. Such threats will ultimately lead to population declines and the loss of crucial genetic variability. Serious threats are posed to endemic species with limited genetic information. In this context, conservation genetics approaches are essential for protecting medicinal plant genetic resources. Molecular marker approaches such as microsatellites, SNPs, and NGS technologies (e.g., MIG-seq) enable more accurate assessments of population structure, variation, and dynamics and help identify priority populations for conservation. This chapter provides an overview of the genetic diversity, threats, and conservation management strategies of medicinal plants, with a particular emphasis on the Sundaland biodiversity hotspot.