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There has been some debate over the question of which types of DNA variation are most appropriate to accurately reconstruct evolutionary events. We compared the capacity of microsatellites (STRs) and various types of single-nucleotide polymorphism (SNP) loci in the chicken genome. The SNP types differ in their location: in exons, introns and promoters. Genetic distances between all possible pairs of 10 populations were calculated for each marker type. STR loci, which are much more polymorphic than are SNPs, are considered to have occurred at recent time compared with old evolutionary events of SNPs. Using structure software, STR loci assigned individuals to their population much more correctly than did any other marker types, whereas SNPs at promoter regions gave the poorest ascription. Furthermore, 29 STR markers were even better than all 152 SNPs together. Ancient evolutionary events that produced genetic differences between the most distant populations such as Red Jungle Fowl and domestic chicken were detected better by exons and introns than by STR loci and promoters. The significant interactions found between marker types and populations suggest that marker types had different phylogenetic histories, possibly related to a different timescale.