Abstract: The recombinant inbred line(RIL) populations derived from Zhenshan 97B/Miyang 46(ZS97B/MY46) and their genetic linkage maps were employed to map QTLs controlling tolerant to high Cu2+ stress at the seedling stage by culturing the seedling in two concentration of Cu2+(100 mg/L and 200 mg/L) on the sand medium.After 20 days of treatment,the relative root length(%) and relative seedling height(%) was measured as index for tolerant to high Cu2+ stress.The results indicated that a total of four main effect QTLs were detected under high Cu2+ stress.Two were significant for the relative root length,qRCC(r)6(100 mg/L) and qRCC(r)9(200 mg/L),the other two were significant for relative seedling height,qRCC(s)1-2(100 mg/L and 200 mg/L) and qRCC(r)6-1(200mg/L).The positive allele were distributed in both the parents.A total of eight pairs of epistasis were detected for tolerant to high Cu2+ stress.Two were for relative root length;the other six for relative seedling height,indicating that epistasis were important genetic basis for the tolerant to high Cu2+ stress at the seedling stage.