The invention discloses valid combinations of 8 novel SSR molecular markers and 2 known SSR molecular markers. The valid combinations are applied to strain identification. DNAs of 22 specific strains are taken as templates, 10 pairs of SSR primers are respectively utilized for carrying out PCR amplification, each pair of SSR primers is subjected to acrylamide gel electrophoresis after the PCR amplification, banding pattern statistic analysis is carried out according to all electrophoretic bands amplified from 22 samples, and therefore, a standard banding pattern of each pair of primers is determined; then the standard banding patterns of 10 pairs of primers of each sample are combined, and molecular identification cards of the 22 different strains of agaricus bisporus are constructed. According to an agaricus bisporus SSR molecular marker specific primer system and an application thereof, the strain identification effect of agaricus bisporus is improved; the agaricus bisporus SSR molecular marker specific primer system and the application are significant for the resource identification, the protection, the development and the utilization of agaricus bisporus.