The QTL qHUS6 for hull silicon content in rice was previously located on the short arm of rice chromosome 6. By using an F2:3 population segregating in the RM587-RM19784 region harboring qHUS6 in an isogenic background, two QTLs for hull silicon content were detected, of which qHUS6-1 was located in the distal region and qHUS6-2 in the region proximal to the centromere. Three rice plants carrying small heterozygous segments in the target region were selected, of which two covered the qHUS6-1 region and the other covered the qHUS6-2 region. Three F2:3 populations were derived from the selfed seeds of the three plants, respectively. QTL mapping was performed using the two populations segregating in the qHUS6-1 region, and qHUS6-1 was delimited to a 147.0-kb region flanked by the markers RM510 and RM19417. Five groups of F3 lines with different genotypic compositions in the qHUS6-2 region were selected from the other F2:3 population. Two QTLs were separated with two-way ANOVA, of which qHUS6-2a was located in the interval defined by RM19706-RM19795 and qHUS6-2b in the interval RM314-RM19665.