Curcuma zedoaria populations comprise 2n = 63 chromosomes with three satellite chromosomes showing elongated secondary constrictions. Flow cytometry results inferred that the 2C nuclear DNA values varied between the populations. The largest genome size was found in the population Chittagong (mean 3.37 pg) and the lowest in the Birganj population (mean 3.15 pg). RAPD based estimations of genetic diversity revealed that hilly populations maintain higher genetic diversity, which was also found to be distinct from plainland and plateauland populations. Genome sizes and genetic diversity values of the populations were positively correlated.