The aim of the present study was to find the best or optimum topology of six chicken populations, which were genotyped based on nine highly polymorphic microsatellite markers. To reach this goal, different genetic distances based on infinite allele model (IAM), stepwise mutation model (SMM) and drawing phylogentic trees on un-weighted pair-group method using arithmetic averages (UPGMA) method were compared. For conducting this research, 16 DNA samples from each Naked Neck (NN), White Silkies (WS), Commercial Layer (CL), Commercial Broiler (CB), Giriraja (GR) and Desi (DS) populations were genotyped for this study. Some of the IAM and SMM based genetic distances showed the same topology under UPGMA. Estimates of different genetic distances revealed relatively close genetic similarity between NN and GR. In the UPGMA-based phylogenetic trees constructed from different genetic distances, four major clusters obtained first, NN and GR; second, NN, GR and CB; third, DS and CL; and forth, WS in a single cluster. The percentage occurrence of each group among genetic distances was 100, 100, 66.7 and 55.6, respectively. The correlation coefficients obtained by Mantel’s test ranged from 0.470 to 0.997 between different genetic distances. In conclusion, by applying this procedure, it is possible to get proper topology using different genetic distances.
