Nuclear microsatellite analysis of Cynopterus was aimed at characterising the microsatellite genotypes and the population structure of this genus especially in the large form of C. brachyotis and the small form of C. brachyotis. Nine pairs of existing microsatellite primers isolated from Indian C. sphinx were used. A total of 51 alleles and 97 genotypes were documented from four forms of Cynopterus. Genetic variations revealed from AMOVA analysis showed that there was low genetic variation among the four forms. The interspecies Global AMOVA comparison analysis showed that the genetic variation between the large and small forms of C. brachyotis was the lowest among interspecies comparisons. This resulted in low genetic structure in the UPGMA tree, and species boundary of each form was not clearly defined. This might due to the microsatellite primers that were isolated from Indian C. sphinx being low in sensitivity to detect variations in Malaysian cynopterans.