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This study was conducted to map quantitative trait loci (QTLs) related to drought stress tolerance. An introgression line population derived from a cross, “Ilpum” / “Moroberekan” was used in this study. F1 plants were backcrossed three times to Ilpum to produce BC3F1 plants. These plants were advanced by selfing for four generation and a total of 117 BC3F5 introgression lines were developed. These lines were evaluated for percent seed set and spikelets per panicle under the control (field) and drought condition. To identify QTLs related to drought tolerance, 134 SSR markers showing polymorphisms between the parents were genotyped for the 117 BC3F5 lines. A total of 6 QTLs associated with drought stress were detected on chromosomes 1, 3, 4, 7 and 10. These include two QTLs for phenotypic acceptability, two QTLs for percent seed set (R2 = 19.0 - 20.9%), and two QTLs for spikelets per panicle (R2 = 22.3 - 23.10%). The Moroberekan alleles at three loci contributed the positive effect for drought tolerance. The SSR markers linked to drought stress tolerance can not only facilitate the selection of valuable genes from Moroberekan, but also allow identification of lines with drought tolerance.