SSR marker is usually the first choice of molecular markers in maize seed identification, but there stills exist some problems for SSR marker, especially in hybrids purity identification. It is still necessary to explore supplementary markers to facilitate varieties identification besides SSR marker. In this paper, SSR and SRAP were performed in 19 maize varieties and 9 samples of Lainong 15 about 1100 individuals. The discriminative power of the markers, genetic relationship and hybrids purity revealed by SSR and SRAP markers were compared and analyzed. Comparing to SSR markers, SRAP markers displayed more amplified alleles per primer-pair, higher PIC value, and higher discriminative power. For the 19 maize varieties, similar clustering results were achieved. Genetic Distance estimated based on SSR and SRAP data were significantly correlated with each other. Specific primers of SSR and SRAP with complementary pattern were used to detect hybrid purity of Lainong 15. The hybrid purity identified by SRAP marker was more vicinal to field test than that by SSR marker. SRAP markers could be applied in maize identification as a useful supplement of SSR, especially in hybrid purity identification.