We examined the role of the hull, seed coat and embryo in the effect of qLG-9, as a first step to elucidate the mechanism(s) responsible for seed longevity in rice. The effects of the other proposed QTLs for seed longevity, qLG-2 and qLG-4, were also investigated. We used chromosome segment substitution lines (CSSLs) derived from a cross between a japonica variety (Koshihikari) and an indica variety (Kasalath) to isolate each QTL. To examine the seed longevity, a germination test was performed after an aging treatment. Both in unhulled and hulled seeds, qLG-9 (located on chromosome 9) increased the seed longevity, unlike qLG-2 and qLG-4 (located on chromosomes 2 and 4, respectively). A germination test using unhulled seeds of the reciprocal crosses between Koshihikari and SL226, the CSSL harboring qLG-9, failed to reveal a maternal effect from the hull or seed coat on the longevity. Thus, it was assumed that the increased seed longevity conferred by qLG-9 was associated primarily with embryonic and/or endospermic factors.