Distantly related species often develop mutations in priming sites of fast evolving gene sequences (e.g. microsatellite loci) over time. Orthologous loci from green-lipped mussel were found to cross amplify the Malaysian giant freshwater prawn, Macrobrachium rosenbergii microsatellites, which indicates a high conservation of flanking sequences. This was confirmed by direct sequencing of target loci. Four microsatellite markers were successfully cross-amplified in the 'western' form of M. rosenbergii with two containing minor interruptions in their sequences. Number of alleles per locus ranged from 5 to 8 with allele frequencies ranging from 0.0048 to 0.2656. Observed heterozygosities ranged from 0.4369 to 0.6848, but in general, these estimates were lower than expected under Hardy-Weinberg equilibrium. Genetic distance values ranged between 0.0059 and 0.1641 with populations in the UPGMA dendrogram not clustering according to their geographical localities.