The invention relates to a molecular marker for japonica rice genetic diversity analysis and an authentication method for the molecular marker. The molecular marker comprises 32 pairs of SSR markers covering 12 chromosomes of paddy rice; each of the fourth, sixth and ninth chromosomes has one marker, each of the fifth, seventh, eighth and tenth chromosomes has two markers; each of the second, third and twelfth chromosomes has three markers; and each of the first and eleventh chromosomes has six markers. The authentication method comprises the steps of a, DNA extraction; b, PCR (polymerase chain reaction) amplification: a PCR reaction system is 15 microlitres and contains 50mM of KCl, 10mM of Tris-HCl(pH8.8), 0.1 percent of Triton-X, 1.5mM of MgCl2, 200mu M of each of NTPs, 0.2mu M of each primer, 5 percent (v/v) dimethyl sulfoxide and 0.5UT of aq DNA polymerase; c, PCR product detection; and d, statistical analysis. According to the molecular marker for japonica rice genetic diversity analysis and the authentication method for the molecular marker, the genetic diversity of a japonica rice material to be detected and genetic difference can be detected, and the molecular markers for the japonica rice genetic diversity analysis are screened.