Microsatellite DNA marker analysis was carried out to assess the population genetic structure of an endangered carp, Labeo calbasu, collected from three different stocks; the Jamuna River, the Halda River and a Hatchery. Four heterologous microsatellite loci (Lr12, Lr14b, Lr21 and Lr24) identified from rohu (Labeo rohita) were analyzed to test the genetic variability of the target kalibaus stocks. The maximum number of alleles observed in loci Lr12, Lr14b, Lr21 and Lr24 were 10,7, 8 and 6, respectively. The loci were found to be polymorphic (