The coconut palm (Cocos nucifera L.), a vital perennial crop, flourishes in tropical and subtropical zones and coastal environments around the globe. The escalating threat of global warming on agricultural systems, particularly on the perennial plantation crops, underscores the need for cutting-edge genomic strategies to protect these plants from diverse biotic stress-induced challenges. Coconut plantations encounter considerable economic risk from pest infestations and disease outbreaks due to their extended life cycle. Consequently, there is an urgent necessity for genomic solutions tailored to creating coconut varieties resistant to biotic stresses. Recent progress in coconut molecular breeding has witnessed the adoption of DNA markers in assessing genetic variation and genetic mapping of quantitative trait loci (QTLs). Advancements have further been made with genomeGenome sequencing and transcriptome analysis technologies, paving the way for leveraging vast datasets derived from coconuts to breed varieties with enhanced tolerance to biotic stress. This chapter evaluates genetic sources available within this species, reviews traditional breeding methods aimed at producing resistant varieties, examines molecular mapping of resistance genes along with QTLs related to marker-assisted selection (MAS), touches upon association studies, provides insights into current genomeGenome assemblies accessible for research purposes and delves into RNA-seq methodologies contributing towards the creation of genotypes resilient against diseases and pests.