Summary Independent origins of cultivated Coconut (Cocos nucifera L.) have been identified in the Old-World Tropics corresponding to the Pacific and Indo-Atlantic oceanic basins. We use unknown coconut cultivated varieties in northern South America to conduct genetic diversity and population structure analysis for the region using single nucleotide polymorphisms (SNPs) markers along the genome and phenotypic data. Analyses revealed two highly genetically differentiated subpopulations corresponding to Pacific and Atlantic oceanic basins. While, this pattern was initially revealed at a global scale, it has now been confirmed at a local scale using genomics in northern South America. We use genotypes identified here to estimate diversification times for main cultivated coconut varieties at a global scale: An early divergent Atlantic tall cultivar, splits from sisters Pacific Tall and Pacific Dwarf cultivars approximately 5400 years ago, while Pacific Tall and Pacific Dwarf cultivars split from a shared common ancestor approximately 1600 years ago. Five loci have been identified as candidate domestication targets, including genes related to vital functions such reproduction, respiration, and defense. These results propose a dated evolutionary hypothesis for the independent origins of cultivated coconut globally were diversification between coconut populations has happened very recently and within few generations.