A technique for obtaining unbiased estimates of genetic parameters (allelic frequencies of RAPD loci, heterozygosity (H), Wright's F statistic, and Nei's genetic distances) in populations of the European (Capreolus capreolus L.) and Siberian (Capreolus pygargus Pall.) roe deer is presented. The technique employs jackknifing and multiple comparative analysis based on a modified Holmes's procedure for Bonferroni's test. It was demonstrated that samples from local groups of roe deer in the Trans-Ural region did not differ significantly in allelic frequencies (0.8, 0.81, and 0.78; P > 0.447) or Nei's genetic distances (0.0056, 0.0273, and 0.0218; P = 0.26), but they could be differentiated based on Wright's F statistic (0.0346, 0.0519, and 0.0450; P = 10(-9)). The parameters of intrapopulation heterozygosity (from 0.18 to 0.042) formed a gradient from the east to the west. Calibration estimates of molecular evolution rate in the family Cervidae obtained based on published data and Jukes-Cantor genetic distances estimated in this study demonstrated that the Siberian roe deer has split into two subspecies, C. pygargus pygargus Pall. and C. pygargus tianschanicus Satunin in the interval between 229 and 462.3 thousand years ago. The species formation of the Siberian and European roe deer was dated between 1.375 and 2.75 Myr ago. Based on the results obtained we recommend the approaches used in the study for analysis of population genetic structure and phylogenetic relationships between populations, subspecies, species, and higher taxa.