In order to provide basic information for restocking program, allelic pattern and diversity in wild stocks of the giant freshwater prawn (Macrobrachium rosenbergii) from Indonesia was studied using microsatellite analysis. The research was performed among the population from nine wildtype populations, Medan (MDN), Padang (PDG), Jambi (JMB), Lampung (LPG), Palembang (PLG), Ciamis (CMS), Palangkaraya (PLK), Samarinda (SMD), and Papua (PPA). Polymerase chain reaction (PCR) with fluorescent label detection showed that a total of 38 alleles were amplified from five primers. The average number of alleles (Na) per locus, observed heterozygosity (Ho), expected heterozygosity (He) and Polymorphic Information Content (PIC) were 11.2, 0.902, 0.664, and 0.666, respectively. The result of the present study of the giant freshwater prawn genetic diversty supports the basic information for broodstock restocking program. On other hand, the wildtype populations from Papua and Palembang displayed the highest genetic diversity and will be preferably used for future selective breeding.