Melia azedarach L. is an ecologically imperative species growing in Thar Desert. Biological effects such as antiviral, anthelminthic, antibacterial etc. makes it important, yet a little is known about its genetic diversity and structure. In this study, 30 RAPD primers were employed for DNA profiling of 47 individuals representing 6 populations from different geographic locales. A total of 87 bands were scored with an average of 2.9 bands per primer. The PIC ranged from 0.1195 to 0.4998 with an average of 0.4160. Nei's genetic diversity (h) and Shannon's information index (I) ranged from 0 to 0.5 and 0 to 0.6931 with an average Nei's genetic diversity of 0.2422. The gene flow (Nm) 1.4381 and the genetic diversity of 0.2381 at species level demonstrated overall high level of genetic diversity. Cladistics analysis using DARwin and Bayesian cluster analysis using STRUCTURE placed 47 individuals into two main clusters or original genetic stocks (K=2) which showed little or no association with the geographic origin. The lack of clear assignment of individuals to geographic regions of sampling and consideration of different populations in the same genetic cluster suggests a recent common evolutionary history.