Phyllanthus emblica is a well-known medicinal and non-timber forest product species, widely distributed in the Indian subcontinent. Multiple disturbances like intensive fruit harvest, the spread of invasive species such as Lantana camara and Taxillus tomentosus, and other anthropogenic disturbances threaten population viability by altering ecological and genetic processes. Studying the genetic diversity and population structure of species harvested intensively and subjected to anthropogenic disturbances is crucial for evaluating their ability to survive under future environmental changes and for establishing conservation strategies. The genetic diversity and population structure of twelve populations of P. emblica that are harvested across three protected areas of the Western Ghats, the world’s most densely populated biodiversity hotspot was evaluated. Three hundred sixty samples were genotyped with nine simple sequence repeat markers. The changes in genetic diversity and genetic structure were assessed between generations by analyzing adults, seedlings, and juvenile samples. Despite intensive harvesting, the results found high genetic diversity in all the populations (mean/pop: Ho= 0.626; Hs = 0.722). However, genetic differentiation was significant between the study regions as well as between adult and seedling populations. The study also indicated a clear clustering of the twelve populations into three distinct genetic clusters. Neighbor-joining tree and hierarchical clustering analysis also showed the same pattern. The genetic data from the study provide information on how local disturbances including harvesting affect the population's genetic diversity and structure, which can provide a basis for implementing programs for conserving and sustainable utilization of P. emblica genetic resources in the future.