Mangosteen in vitro plantlets derived from seed have been produced, however an investigation on the somaclonal variation among these plantlets has not been reported before. Detection of somaclonal variation among mangosteen plantlets using Randomly Amplified Polymorphic DNA marker requires the amplification of any DNA segment using short oligonucleotide primers of arbitrary nucleotide sequence and polymerase chain reaction procedures. The objectives of this study are to select primers that produce reproducible polymorphic bands and to optimize each polymerase chain reaction component. A total of 29 primers were screened and 21 of them amplified polymorphic bands. Of the 151 bands obtained, 102 were polymorphic bands and 49 were monomorphic bands ranging between 182 bp – 3320 bp. The percentage of monomorphic bands ranged between 0% - 77.8% whereas the polymorphic bands were between 22.2% - 100% for all primers tested. The highest number of scorable bands was produced using primer AP-20 while the lowest was by OPA-7. The highest percentage of polymorphic bands (100%) was generated by AB-16 whilst the lowest percentage (22.2%) was produced by OPA-5. The optimized of each PCR component for Randomly Amplified Polymorphic DNA is MgCl2 2 mM, Primer 4 µM, dNTP-mix 0.4 mM, Taq polymerase 1.5U/µL, DNA template 40 ng/ µL. Amplification reaction was run for 40 cycles following the cycle program i.e. initial denaturation at 94oC for 5 minutes, denaturation at 94oC for 30 seconds, annealing at 37-38oC for 1 minute, extension at 74oC for 2 minutes and final extension at 72oC for 5 minutes.