Morinda tinctoria (Rubiaceae) commonly called as ‘Indian Mulberry’ is one of the avenue trees of historically important Mandore garden planted anthropogenically in the past. Objective of this study was to determine the genetic diversity of M. tinctoria population at Mandore garden using Random Amplified Polymorphic DNA and Inter Simple Sequence Repeat Markers. A total of 97 bands were produced from 10 random amplified polymorphic DNA primers (49 bands) and 8 inter simple sequence repeat primers (48 bands). No polymorphic bands were obtained in any accessions using the two methods, which strongly suggested that M. tinctoria of this region appear as identical clones. Monomorphic pattern revealed the clonal plantation of M. tinctoria in this historical garden. This is the first report on use of molecular markers to infer the ancient plantation history. Consequences of genetically monomorphic population under global climate changes are discussed and conservation strategy is proposed.