Photoperiod-sensitive genic male sterility (PSGMS) rice has a number of desirable characteristics for hybrid rice production. In this study, we conducted a molecular marker-based mapping and genetic analysis of PSGMS genes using two crosses involving the original mutant Nongken 58S as the PSGMS parent. The genomic locations of the PSGMS loci were determined following the "bulked extreme and recessive class" approach, in which the regions containing the PSGMS loci were identified by assaying the bulks of extreme phenotypes and the distances between the PSGMS loci and molecular markers were calculated from the highly sterile plants of the F2 populations. Two PSGMS loci, located on chromosomes 7 and 12, respectively, were identified in both crosses. The locus on chromosome 7 was the same as pms1, identified previously in a cross between an indica PSGMS line and an indica cultivar. The one on chromosome 12 was a new locus that we designated as pms3 Both loci had major effects on fertility and acted like a pair of classical duplicated genes in controlling male sterility. Comparison of the present finding with previous results indicated a complex genetic basis of PSGMS. The implications of such genetic complexity in breeding for PSGMS lines are also discussed.