Marker-assisted selection (MAS) offers a powerful method for optimizing the development of diseaseresistant oil palm (E. guineensis Jacq.). An efficient and cost-effective approach involves investigating the genetic basis of resistance by directly exploiting data from ongoing breeding programs. Our results on Fusarium wilt, caused in Africa by Fusarium oxysporum F. sp. elaeidis, and on Basal Stem Rot (BSR), caused by Ganoderma boninense in Southeast Asia, illustrate the potential of this approach for identifying the genomic regions responsible for oil palm disease resistance. They provide key information not only on the genomic regions targeted by MAS, but also on the complexity of the genetic architecture of disease resistance, the genetic sources of favourable alleles, and the potential relationships between different traits of interest. MAS leverages as well knowledge of pathogens. In this context, the G. boninense–oil palm pathosystem is attracting increasing interest within the scientific community. An early inoculation test, enabling the induction of BSR in young seedlings under controlled conditions, allowed the identification of resistance Quantitative Trait Loci (QTL). This method, commonly used for selecting partially resistant progeny, allows for functional studies on the interactions between G. boninense and oil palm. Pathogen's genetic diversity data have led to a better understanding of the importance of sexual reproduction, scale of spore dispersal and of the demographic dynamics of the species in South- East Asia. A transcriptomic study performed on artificially inoculated oil palms showed that G. boninense expresses enzymes already known to be involved in the aggressiveness of other white rot fungi like CAZymes wood decay enzymes and detoxification proteins. The complete genome sequence of G. boninense further enhances our knowledge.