PeiAi64S, a photoperiod and thermo-sensitive genic male sterile, has been wildly applied to hybrid rice seed production in China, but its photoperiod-sensitivity gene for heading date 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, using heading time nearly isogenic lines EGO - EG7, ER - LR, T65 - T65m and six heading date QTL-isogenic lines, NIL (Hd1) - NIL (Hd6) with the genes of Nipponbare but Hd1 - Hd6 genes from Kasalath respectively, we performed a genetic analysis of PeiAi64S with special reference to photoperiod-sensitivity loci, in natural long days at Nanjing (32 degrees N) where the average day-length is about 14 h and in natural short days at Linshui county, Hainan province(18 degrees 29'N), where the average day-length is about 11.6 h during the course of rice growing respectively. The F1 and F2 generations from the crosses 'PeiAi64S x heading time nearly isogenic lines' were subjected to genetic analyses. Experimental results showed that PeiAi64S carries photoperiod-sensitivity allele gene E1 and E3 and dominant earliness gene Ef-1 in E1 and E3 and Ef-1 loci, respectively, and a photoperiod insensitivity allele Se-1 degrees in Se-1 locus. Meanwhile, the photoperiod-sensitivity gene E1 and photoperiod-insensitivity gene Se-1e in PeiAi64S were also identified by crossing with the NIL(Hd1) and NIL(Hd4). In addition, a recessive inhibitor for photoperiod-sensitive gene E1 or Se-1(n) and other modified photoperiod-sensitive genes: i-Se-1, E3, Hd3 (En-Se-1), Hd5 and Hd6, were identified in PeiAi64S by crossing with QTL nearly isogenic lines: NIL(Hd2), NIL (Hd3), NIL (Hd5) and NIL( Hd6), The results indicated that the genotype of PeiAi64S's heading date was: E1E1e2e2E3E3Se-1(e)Se-1(e)Ef-1 Ef-1 i-Se-1 i-Se-1.