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[Objective] The research aimed to clarify the genetic mechanism of special wide compatibility of GC13.[Method] The clustering analyses of GC13,five indica,five japonica and five wide compatibility varieties were carried out by using 70 SSR primers.[Result] GC13 was clustered into japonica group and had far genetic relationship with indica and wide compatibility variety.Two fertility loci were detected in GC13,in which one closely linked to RM225 on chromosome 6.According to the position on the chromosome,it speculated that this locus was allelic to S5.GC13 carried the allelic gene S5-n at this locus.The other locus closely linked to RM408 on chromosome 8 and was provisionally designated as Sg（t）.At this locus,GC13 carried Sg（t）-i allelic gene,which was consistent with IR36.The effect of S5 locus was stronger than that of Sg（t）.[Conclusion] The research laid the good foundation for using the wide compatibility line GC13 to breed the hybrid between subspecies.