A recombinant inbred line (RIL) population and two chromosome segment substitution line (CSSL) population derived from the cross of Asominori (japonica) and IR24 (indica) were used to detect QTL controlling seed dormancy. CSSL1 were a series of IR24 chromosome segment substitution lines in Asominori background, and CSSL2 were a series of introgression lines of Asominori in the background of IR24. Three QTL were detected on chromosome 3, 6 and 9 in RIL population, and individual QTL accounted for between 12.3% and 13%. Three QTL were detected on chromosome 1, 3 and 7 in CSSL1, and individual QTL accounted for between 11.5% and 18.9%. Three QTL were detected on chromosome 1, 2 and 7 in CSSL2, and individual QTL accounted for between 11% and 16%. The QTLs on chromosome 1 and 7 were detected in CSSL1 and CSSL2 populations simultaneously, QTL came from Asomonori, the moderate dormant cultivar, increased seed dormancy, and QTL from IR24, the weakly dormant cultivar, decreased seed dormancy. It can be deduced that there exist genes controlling seed dormancy at this region.