The ORF100, ORF29-TrnC(GCA) spacer, rps16 gene intron and TrnT(UGU)-TrnL(UAA) spacer of chloroplast DNA (cpDNA) of 6 photoperiod-sensitive genic male sterile (PGMS) rice, Nongken58S and its 5 derivatives, were amplified and sequenced. According to the result of ORF100 and ORF29-TrnC(GCA) spacer analysis, the cpDNA of japonica PGMS line Nongken58S was Japonica, and among those PGMS lines derived from Nongken58S, cpDNA of japonica 7001S and 3 indica lines 1103S, Peiai64S and Guangzhan63S were that of japonica, which was in accordance with the cytoplasm pedigree provided by their breeders. But the cpDNA of indica PGMS line W6154S was that of indica, which disaccorded with the cytoplasm pedigree, so we conjectured that the breeders had used the PGMS line as the male parent. Basing on the result of sequence analysis, we found single nucleotide polymorphism in rps16 gene intron and TrnT(UGU)-TrnL(UAA) spacer of these 5 japonica PGMS lines.