In Eucalyptus forests, drought stress has being pointed as one of the most important abiotic factor significantly affecting the growth and yield. The use of drought tolerant genotypes can be the most reasonable alternative to overcome this problem. Drought tolerance is a complex trait and QTLs mapping approach can help to understand the genetic control related to this trait. This study aims to identify genetic loci linked to phenotypic variation in drought tolerance in a segregant progeny grown under two different irrigation conditions. The progeny was generated from a cross between two contrasting hybrid (E. grandis x E. urophylla) to water stress. The experiment took place in a greenhouse under two irrigation conditions. Physiological traits were measured and QTL mapping analyses will be performed based on BLUPs. Two genetic maps were obtained using different set of markers and two software. The linkage analysis executed on OneMap resulted in 14 groups with 116 markers (SSR, SSR-EST and AFLP). The map’s length was 1569.5 cM with an average distance of 12.4 cM between the markers. Using JoinMap, the length of the consensus map was 770 cM with an average distance of 7.2 cM between 101 markers in 11 groups. Significantly differences in the number of linkage groups, length and average distance between the markers were observed. The QTLs analyses were performed and allowed to identify some loci which can contribute to phenotypic variation in eucalyptus drought tolerance.