Acrocarpus fraxinifolius is an important tropical timber species mainly found in Asia and is a fast growing tree species found naturally in India, Chaina, Burma and Sumatra. In Karnataka, the species is extensively cultivated in coffee plantations due to its desirability in the rainy season that favours coffee growth. The species is also to the smaller extent noticed in natural forests and sacred groves of Kodagu district, Karnataka, India. However there was no much studies were taken in assessing the genetic diversity of the species exists in natural forests, sacred groves and coffee plantations. Hence the study was undertaken to know the extent of genetic diversity in the species as comparing to natural forests, sacred groves and coffee plantations was analyzed using ISSR markers. The leaf samples were collected from each of landscape. DNA was extracted from leaf material using Cetyl Trimethyl Ammonium Bromide (CTAB) technique. A total of 24 ISSR markers were used for this study, but only 14 ISSR primers were successfully amplified for 8 samples. Sampled populations from all the three landscapes showed relatively higher diversity. While the sacred grove and coffee plantations populations recorded higher diversity (0.3779 and 0.5601: 0.3661 and 0.5403, respectively) than natural forest population (0.2982 and 0.4567). This data clearly suggests that the farmers have conserved a higher level of diversity.