Fusarium crown rot (FCR) is a serious cereal disease in semi-arid regions worldwide. In assisting the effort of breeding cultivars with enhanced resistance, we identified several barley genotypes with high levels of FCR resistance. One of these genotypes, AWCS079 which is a barley landrace originating from Japan, was investigated by developing and assessing three populations of recombinant inbred lines. Two QTL, one located on the long arm of chromosome 1H (designated as Qcrs.cpi-1H) and the other on 3HL (designated as Qcrs.cpi-3H), were found to be responsible for the FCR resistance of this genotype. Qcrs.cpi-1H is novel as no other FCR loci have been reported on this chromosome arm. Qcrs.cpi-3H co-located with a reduced height (Rht) locus and the effectiveness of the former was significantly affected by the latter. The total phenotypic variance explained by these two QTL was over 60 %. Significant effects were detected for each of the QTL in each of the three populations assessed. The existence of these loci with major effects should not only facilitate breeding and exploitation of FCR-resistant barley cultivars but also their further characterization based on fine mapping and map-based gene cloning.