One of the problems faced in coconut cultivation is the lethal yellowing disease. Experimental trials, conducted in endemic region, showed that the Vanuatu Tall and Sri-Lanka Green Dwarf genotypes were tolerant while the West African Tall appeared susceptible to the lethal yellowing disease. Genetic differences between these tolerant genotypes and the susceptible ones were evaluated using twelve microsatellite markers. This work aimed to use identified materials as reference to select suitable parents for gene mapping studies. A total of 58 alleles were detected at the 12 microsatellite loci. The number of alleles varied from 3 to 7, with an average of 4.83 alleles. The Fst index revealed that 59.70% of the total allele variability explained differences between the three accessions. Genotypes of West African Tall, susceptible to the lethal yellowing disease, were less genetically clustered to the genotypes of the two tolerant accessions. This differentiation was based on specific alleles and frequency variation of shared allele in the three accessions. This molecular typology was useful as reference for large molecular screening of coconut genetic resources and the identification of suitable parents for the development of mapping populations for tagging the lethal yellowing resistance genes.