A total of 386 long-tailed macaques (M. fascicularis) from 17 populations in Malaysia was analysed using eight polymorphic microsatellite loci on a microfluidic-based platform (Agilent DNA 1000 Chips on the Agilent 2100 bioanalyzer) to identify and evaluate the genetic polymorphism and population structure. The microfluidic-based chip platform provides simple, reliable and cost effective approach for microsatellite studies. Genetic diversity estimates showed that the Peninsular Malaysian populations are slightly more diverse than their Bornean conspecifics. Furthermore, weak population structuring among the peninsula populations suggest that they comprise of genetically contiguous populations. The Sarawak and Labuan populations were differentiated from the peninsula populations except for the Sabah population which is due to the low sample number from the latter. Interestingly, no matching genotype was found among all samples indicating that the loci set can be used for individual identification of M. fascicularis
