Melia azedarach L. (Chinaberry) is fleshy fruited small to medium sized tree native to China and North Western India. It grows in Pakistan and Turkey in various areas facing great environmental changes to maintain its survival. The species is valued for its high quality wood, medicinal, ornamental and shade purposes. The present work was aimed to estimate the genetic variation among the populations of Melia azedarach that were collected from five different locations in Turkey and three different locations in Pakistan. 14 RAPD primers producing polymorphic and monomorphic bands were analyzed. Genetic distances were calculated for all the species studied by RAPD-PCR. The lowest genetic similarity and the highest genetic polymorphic values were determined. It was observed that there is a clear split among populations from different areas in Turkey and Pakistan. These differences may be due to eco-geographical association with genetic variation and should be conserved to retain the genetic diversity of the species. Appropriate conservation strategies were suggested in conclusion.