The genomes of domestic and jungle fowl populations maintained in Ukraine and Germany were screened using microsatellites as molecular markers. Genetic variation and genetic distances between strains of different origins and performance potentials were determined. In total, 224 individuals of 20 populations were genotyped for 14 microsatellite markers covering 11 linkage groups. Of the 14 microsatellite loci, the number of alleles ranged between 2 and 21 per locus, the mean number of alleles being 11.2 per locus. By using Nei's standard distance and the Neighbor-Joining method, a phylogenetic tree was reconstructed; its topology reflected general patterns of relatedness and genetic differentiation among the chicken populations studied. Three major phylogenetic tree groupings were found. The red jungle fowl (Gallus gallus) formed a separate branch and demonstrated a specific allele distribution when compared with domestic fowl breeds analyzed. The second branch comprised commercial layer lines and chicken breeds that were subject to intense selection in the past or had common ancestral breeds with commercial strains. The third group encompassed the German native breed populations. The information about population and breed genetic relationships estimated by microsatellite analysis may be useful as an initial guide in defining objectives for designing future investigations of genetic variation and developing conservation strategies.