Genetic alterations of maize landrace cv. Tiaohuanuo populations having different germination levels were analyzed using agronomic traits and SSR markers. It showed that the proportion of plant with different coleoptile and leaf sheath colours varied with the decline of germination percentage. When seed germination percentage declined to 32%, there was no light-purple coleoptile plant. On the other hand, the proportion of light-purple leaf sheath plant increased while the white leaf sheath plant decreased when seed germination percentage declined. The percentage of polymorphic bands, the number of alleles (na), effective number of alleles(ne), Nei's gene diversity index(h)and Shannon's information index(I) were lower in artificially aged population with lower germination percentage than in CK population with higher germination percentage using SSR. This indicated that the genetic diversity was lower in aged populations than in CK population. The result also showed that a low germination percentage standard for regeneration is disadvantageous for maintaining the genetic integrity of heterogeneous germplasm.