In this study, we isolated microsatellite DNA from the Huoyan goose genome with magnetic beads. As a result, 150 positive clones were identified, and 148 microsatellites were found. Among the 148 microsatellites, 69.6% were perfect, 17.6% were imperfect, and the rest were compound type (12.8%). Twenty microsatellite primers were used to screen 90 individuals from 3 Huoyan goose populations. Eight loci were polymorphic with a low number of alleles (2 to 4). The observed and expected heterozygosities ranged from 0.3556 to 1 and from 0.2923 to 0.6868, respectively. All the 8 polymorphic loci were in Hardy-Weinberg equilibrium. These molecular markers will be useful for future studies on population genetic structure and conservation genetics in Huoyan geese.