Zhenshan 97A, a rice male sterile, were applied widely since the release of hybrid rice in 1973 in China, but the genotype of heading time in this sterile line was still unknown. This definitely limited the further use of this sterile line in breeding practice and re-production of hybrid seeds. To solve this problem, we analyzed the segregation pattern of phenotype of heading time in progenies from crosses between Zhenshan 97A and four tester cultivars, Akihikari (e1e1e2e2e3e3 Se-1eSe-1e), Koshihikari (E1E1E2E2e3e3Se-1eSe-1e), Nipponbare (E1E1e2e2e3e3Se-1Se-1) and Hinohikari (E1E1E2E2e3e3Se-1Se-1), whose genotypes of heading time were already known. The results showed that the genotype of heading time in Zhenshan 97A was e1e1e2e2E3E3Se-1Se-1 and it also carried a recessive inhibitor i-Se-1 for phtoperiod-sensitivity. Meanwhile, a major photoperiod-sensitive dominant genes Se-1 and other modified photoperiod-sensitive genes: i-Se-1, E3, Hd3(En-Se-1), Hd5 and Hd6, were identified in Zhenshan 97A by crossing with QTL nearly isogenic lines: NIL (Hd1), NIL (Hd2), NIL(Hd3), NIL(Hd5) and NIL(Hd6).