Lethal yellowing (LY), a disease associated with the presence of phytoplasmas, is currently the most important threat to coconut cultivation in many production sites worldwide. It causes considerable losses, due to the death of the majority of infected palms. Control involves agronomical measures (elimination of potential reservoirs, early eradication of affected palms, among others), combined with the use of less susceptible varieties. In order to identify the genomic region linked to the survival of LY infected plants, a case-control genome wide association approach was used. After identifying survivors in LY affected fields in Ghana, a sample of sawdust was collected for DNA extraction. As controls, plants from uninfected nearby fields were also collected. After DNA extraction and SNP calling using a new 2.06Gb long reference genome (data not published), a region on the long arm of chromosome 8 was identified by five different statistical models as significantly associated to the survival phenotype. A haplotype analysis allowed to identify the alleles of four highly linked markers associated with the survival, and 24 individuals bearing this allelic combination. The identification of this genomic region linked to the survival to LY opens the perspective for breeding programs to introduce this important trait to other key varieties.