Ceratocystis wilt (CW) in cacao (Theobroma cacao L.), caused by Ceratocystis cacaofunesta, is a drastic disease that results in plant death. The pathogen was recently identified in the major cacao-producing region of Brazil-Bahia. The identification of genetic markers tightly linked to disease resistance loci is a valuable tool for the development of resistant cultivars using marker-assisted selection (MAS). Branches of 143 six-year-old individuals of an F2 Sca 6 × ICS 1 population were wounded by making a 3-mm deep cut with a sterile scalpel, and inoculated with a 20-?l drop of a spore suspension of 3 × 104 CFU/ml. The inoculation method used allowed the population to be quantitatively phenotyped. The length of the xylem discoloration followed a continuous distribution. These results imply that the resistance was quantitatively inherited. Quantitative trait loci (QTL) analysis revealed two genomic regions (in linkage groups 3 and 9) associated with CW resistance. The QTL explained individually from 6.9 to 8.6 % of the phenotypic variation. The QTL identified are crucial for identifying genes for resistance and can be applied in the genetic breeding of cacao using MAS.