Summer mortalities of the Pacific cupped oyster Crassostrea gigas have been described in the literature for decades. One solution to overcome this problem would be to select animals more tolerant to summer mortalities, as this trait was shown to be highly heritable (Degrémont, 2003). Such selective breeding would strongly benefit from the identification of markers associated to the resistance to allow the development of markers assisted selection. Recently, a set of a new kinds of markers (SNPs) have been developed in the Pacific oyster. These markers were identified and characterized in several genes involved in the immune response and energetic pathways (Sauvage, 2007). In this context, the mapping of SNPs, of 16 new EST-SSR based markers and of previously published SSR will increase the density of the linkage map and consequently the accuracy of QTL mapping. To reach this objective, linkage maps were built one three F2 segregating oyster families showing a strong differential response during the summer mortality event in 2006. Moreover, two traits, e.g. the mortality and the viral load in Herpes Virus (OsHV1) measured by Q-PCR (Pépin, submitted) have been used to detect candidate loci through a QTL analysis. Our preliminary results show at least two candidate loci that correlates with the viral load in Herpes virus. Currently, we are screening additional candidate loci to get a better understanding of the complex genetic architecture that relies under these two traits during the summer mortality phenomenon in the Pacific oyster.