Coconut belongs to a typically South American subtribe (Attalinae), yet at the dawn of agriculture, it was in both the Indian and Pacific Oceans. How it reached this pre-historic distribution remains unclear. During the last 20 years, molecular markers have been developed to study coconut genetic diversity, assess gene flows and identify markers of agronomic traits. They have proven useful to identify coconut cultivars and to track genetic exchange between populations and human migrations. Two well-differentiated gene pools, originating from the Indian and the Pacific Oceans, were identified. Self-pollinating Dwarf coconuts resulted from a single domestication event in Southeast Asia. Markers for various agronomic traits were identified through linkage mapping and association studies. More recently, genome expression was studied in various organs, providing a representation of the coconut proteome and of its regulation, allowing to identify key genes involved in the metabolism of the endosperm and in somatic embryogenesis. Several research teams undertook its sequencing, and two draft sequences have been published. This large genome was recently assembled into 16 pseudomolecules by anchoring it on a linkage map. The biology of the coconut makes genetic improvement difficult. Genomic selection and marker-assisted selection can speed up the first stages of varietal development based on advanced generations of crosses between genetically distant populations. This will require profound changes in the methods used in field observation, aiming to acquire more phenotypic data at the individual level as well as the open availability of genomic resources.