Identification of genetic factors controlling traits associated with seed germination under drought stress conditions, leads to identification and development of drought tolerant varieties. Present study by using a population of F2:4 derived from a cross between a drought tolerant variety, Gharib(indica) and a drought sensitive variety, Sepidroud(indica), is to identify and compare QTLs associated with germination traits under drought stress and non-stress conditions. Through QTL analysis, using composite interval mapping, regarding traits such as germination rate(GR), germination percentage(GP), radicle length(RL), plumule length(PL), coleorhiza length(COL) and coleoptile length(CL), totally 13 QTLs were detected under pole drought stress(-8 MPa poly ethylene glycol 6000) and 9 QTLs under non-stress conditions. Of the QTLs identified under non-stress conditions, QTLs associated with COL(qCOL-5) and GR(qGR-1) explained 21.28% and 19.73% of the total phenotypic variations, respectively. Under drought stress conditions, QTLs associated with COL(qCOL-3) and PL(qPL-5) explained 18.34% and 18.22% of the total phenotypic variations, respectively. A few drought-tolerance-related QTLs identified in previous studies are near the QTLs detected in this study, and several QTLs in this study are novel alleles. The major QTLs like qGR-1, qGP-4, qRL-12 and qCL-4 identified in both conditions for traits GR, GP, RL and CL, respectively, should be considered as the important and stable trait-controlling QTLs in rice seed germination. Those major or minor QTLs could be used to significantly improve drought tolerance by marker-assisted selection in rice. Identification of genetic factors controlling traits associated with seed germination under drought stress conditions, leads to identification and development of drought tolerant varieties. Present study by using a population of F2: 4 derived from a cross between a tolerant variety, Gharib (indica) and a drought sensitive variety, Sepidroud (indica), is to identify and compare QTLs associated with germination traits under drought stress and non-stress conditions. Through QTL analysis, using composite interval mapping, regarding traits such as germination rate (GR), germination percentage (GP), radicle length (RL), plumule length (PL), coleorhiza length (COL) and coleoptile length (CL), totally 13 QTLs were detected under pole drought stress (-8 MPa poly ethylene glycol 6000) and 9 QTLs under Of the QTLs identified under non-stress conditions, QTLs associated with COL (qCOL-5) and GR (qGR-1) explained 21.28% and 19.73% of the total phenotypic variations, respectively. QTLs associated with COL (qCOL-3) and PL (qPL-5) explained 18.34% and 18.22% of the total phenotypic variations, respectively. A few drought-tolerance-related QTLs identified in previous studies are near the QTLs detected in this study, and several QTLs in this study are novel alleles. The major QTLs like qGR-1, qGP-4, qRL-12 and qCL-4 identified in both conditions for traits GR, GP, RL and CL, respectively , should be considered as the important and stable trait-controlling QTLs in rice seed germination. Those major or minor QTLs could be used to significantly improve drought tolerance by marker-assisted selection in rice.