It is very necessary in science and application to resolve SNP genetic information in experimental duck genomes by means of WGRS technology. In this study, we present WGRS analyses of three common SPF experimental ducks, including Jinding duck (JD), Shaoxing duck (SX), and Fujian shanma duck (FJ). The main objectives of this study were (i) to construct a database of SNP genetic information of three experimental duck genomes (ii) to screen common SNP loci as marker loci for genetic quality detection and (iii) to compare the important genomic regions and molecular markers of different experimental duck breeds. Our results provide an important resource for the establishment of a rapid and automatable technical system for genetic quality detection of agricultural experimental ducks.