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Drought is one of the major limiting factors in sustainable maize production all over the world. In order to develop maize variety with drought tolerance, it is necessary to explore the genetic basis and map the quantitative trait loci (QTLs) controlling the yield and associate agronomic traits under semi-arid land condition. In this study the QTLs for flower time, plant height, yield and yield components were characterized with recombinant inbred lines (RIL) derived from the cross 5003 x p138 under drought stress and well-watered regime in the years 2004 and 2005, respectively. A linkage map was constructed based on 101 simple sequence repeat (SSR) markers covering a total of 1395.2 cM genetic distance, and an average distance of 13.81 cM between markers. A total of 51 QTLs were identified for 10 traits on 10 different chromosomes. Under the well-watered regime, 25 QTLs were identified for 9 traits, whereas under the water-stressed conditions, 22 QTLs were found for 7 traits. Four QTLs for drought tolerance index were found. Phenotypic variation associated with each QTL ranges from 1.68 to 13.3%. The results reveal that most related traits cluster in chromosomal blocks: bnig1614-bnig1083 on chromosome 1 and bnig1634-bnig1209 on chromosome 9 for plant height, bnig1035-bnig1564 on chromosome 1 for yield and its components and drought insistence index, near NC012 and bnig2907-bnig1136 on chromosome 6 for flower time and anthesis-silking interval (ASI), and near bnig1063 on chromosome 5 and bnig1241 on chromosome 4 for flower time. Four QTLs for male flower time were identified in marker bnig1327-bnig1812 on chromosome 8 under two water regimes. These QTLs may be useful for the marker-assisted selection in maize breeding for drought resistance.