Cultivated rice (Oryza sativa) is comprised of two subspecies: indica and japonica, which differ in agricultural traits, physiological characteristics and ecological adaptation.Chlorate resistance is one of the reliable physiological characters in indica-japonica classification, in which indica is generally more sensitive to chlorate than japonica.Understanding of genetic basis of chlorate sensitivity is important for revealing the evolutionary mechanism of indica-japonica differentiation and distinguishing indica from japonica with new developed DNA markers, therefore.