Effective population size is a crucial concept of conservation biology. It is reduced by biased sex ratio, consequently causing loss of genetic variation. To evaluate genetic diversity related to gender, and investigate the possible effects of biased sex ratio, we analyzed available microsatellite DNA markers from 120 samples of Populus nigra L (European black poplar) originating from five geographical regions in Turkey. Using 12 microsatellite markers, we detected 60 clones of the same genotype, out of 120 trees. The clone genotype was observed both in males and females, which might suggest that P. nigra deviates from dioecism. Three genetic clusters were detected, two of which possibly correspond to commercially available trees. Overall allelic richness was found to be similar for both genders, whereas heterozygosity was slightly higher in males. Additionally, a simulation software prototype was developed to see the effects of sex ratio on diversity and allele frequency trends in future generations, given the available molecular data. Results showed that if biased sex ratio persists, allele loss and fixation might occur in a higher rate, causing loss of variation.