Vascular-Streak Dieback (VSD) disease of cacao, caused by the fungus Ceratobasidium theobromae, has devastating impacts on cacao production in southeast Asia and Oceania. This study aimed to identify genomic regions associated with resistance to VSD using a population derived from a cross between the cocoa genotypes S1 (VSD resistant) and CCN51 (VSD susceptible). QTL analysis was performed using a genetic linkage map constructed with 8,698 DArT markers and 1,470 SNP markers. Two QTL were detected, one on linkage group 8 and the other on linkage group 9. The QTL on linkage group 8 explained 15-16% of the phenotypic variation while the QTL on linkage group 9 explained 16-18% of the phenotypic variation. Five polymorphic microsatellite (SSR) markers were identified within the QTL regions. SSR markers showed clear polymorphism among the VSD resistant and susceptible lines in the two populations, S1 x CCN51 and CCN51 x M07. These results suggest that these markers could be closely associated with VSD resistance and therefore used in marker-assisted selection for cacao breeding programs in response to VSD disease. Further, genomes of the S1 and CCN51 genotypes were sequenced using paired end short reads. Both S1 and CCN51 whole genome sequencing generated 383 and 367 million clean reads, respectively, and 93% of reads from both S1 and CCN51 mapped to the reference genome Matina 1-6. Alignment to the reference genome enabled the detection of 1.87 million polymorphic SNVs/Indels and 8,363 polymorphic structural variants (SVs) among the two genomes. The resequencing of the genomes of cacao genotypes S1 and CCN51 provides a valuable resource to narrow the search for candidate genes that underlie VSD resistance.