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Grain protein content (GPC) in durum wheat is a crucial determinant of pasta quality and as such is an important economic factor. This study was carried out to determine the microsatellite markers (SSRs) as associated with GPC in durum wheat grown under normal and moisture stress conditions. F3 and F4 population derived from 151 F2 individuals developed from a cross between Oste-Gata (drought tolerant) and Massara-1 (drought susceptible) genotypes, were used. The population was evaluated under four environmental conditions (two irrigation regimes in two growing seasons). The results of single marker regression analysis (SMA) revealed that 2, 4 and 10 markers to be associated with GPC, test weight (TW) and 1000 grain weight (TGW), respectively. These markers explained between 4.4 and 21.8% of the phenotypic variation in either environmental condition. The most significant marker observed for GPC was located on 5B chromosome near Xgwm408 under normal conditions and the other marker was observed on 1A, explaining about 15% of phenotypic variance. However, it was not recognized any marker related to GPC under drought stress conditions. Xgwm408 marker was coincident with the markers identified for TW, TGW and components of grain yield under drought stress conditions. In spite of 5B, the other chromosomes such as 2B and 3B were related to quantitative traits like TW and TGW. Composite interval mapping (CIM) identified 4 and 5 putative minor and major QTL for TW and TGW, respectively. Two QTL near Xbarc101 and Xbarc124 markers on 3B and 2B chromosome, explained up to 45.2 and 6% of phenotypic variations of TGW and TW, respectively.