Fat content is a concern for the enhancement of rice for eating, cooking, and storage qualities. To clarify its genetic mechanism, a double haploid (DH) population derived from anther hybrid F 1 of Zhenshan 97B (indica) and Wuyujing 2 (japonica) and two backcross F 1 (BCF 1 ) populations, which came from the DH lines backcrossing to two parents, were used to scan quantitative trait loci (QTLs) and dissect gene effects for the crude fat content (CFC) in brown rice. Fourteen QTLs were resolved, distributing on chromosomes 1, 3, and 5-9. Three loci were detected repeatedly in two populations, DH or BCF 1 . Among these loci, a major QTL, qCFC5, flanking markers RM87 and RM334, was located on chromosome 5, which was detected simultaneously among three populations. The main QTLs had a major role in controlling CFC in brown rice and were modified by several mini-effect QTLs and epistatic affection.