Coconut is the most important cash crop along the Coast of Kenya, yet its genetic diversity has not been fully established. Genetic diversity study of 48 coconut genotypes, collected at the Coastal Kenya was conducted with 13 polymorphic short sequence repeats (SSRs) markers. SSR analysis was performed using GeneMapper while data analysis was done with PowerMarker and DARwin softwares. Analysis revealed a total of 68 alleles ranging from 2 to 11 per locus with a mean of 5.23 per marker. Gene diversity and polymorphic information content (PIC) ranged between 0.41 to 0.83 and 0.33 to 0.79, respectively. Neighbour -joining dendrogram grouped the genotypes into three major clusters with distinct sub-clusters. This study underscored that capillary electrophoresis is a more accurate and informative technique for SSRs allele scoring as opposed to agarose gels. The clusters observed forms the basis to isolate conservation blocks, which is key to establishing a genebank, since there is no documented coconut genebank for ex-situ conservation in Kenya.