Studies to determine the genetic bases to witches´ broom resistance were being carried out in order to identify different genetic sources of resistance and to improve the efficiency of selection using molecular markers. Scavina-6, particularly in the cocoa producing region of the Bahia state in Brazil, was initially the main resistance source. A major QTL of resistance was detected in the linkage group 9 from a F2 Scavina 6 x ICS1 progenies (Brown et al 2005 and Faleiro et al 2006). Observations related with the number of vegetative brooms and flower cushions brooms, were carried out on143 individuals replicated three times by grafting on CEPLAC-hybrids and observed over a period between 2003 and 2008. Analyses were made with SAS, mainly to adjust phenotypic values (number of brooms ) by a regression taking into account the difference of the section of each plant (vigor was made in 2008 assessing the section of the grafted portion). QTLs analyses were carried out with MapQTL.5 software. We confirm the presence of the previous QTL located in the LG9 around the mTcCIR35 marker. However, the LOD score and the percentage of variation explained by the QTL significantly decrease over time and change its position into the confidence interval. During this new period of evaluation of the disease in the field, others QTLs of resistance were also detected. The QTLs values related to these others significant QTLs of the resistance to WBD and to a QTL involved in the vigor were also presented. This result suggests a change in the relationship between the host and the pathogen.