This study was conducted to assess the molecular diversity of eight NJM x GVT coconut palm (Cocos nucifera L) hybrid progenies and a BP121+ hybrid control using 15 microsatellite loci. The NJM x GVT hybrids are tolerant to the Lethal yellowing coconut disease when the control is very susceptible to the disease. As a result of this work, 86 alleles were identified at the 15 microsatellite loci with a variation of 2 to 11 alleles per locus. The intra-progeny diversity (HS = 0.50) is higher than the inter-progeny diversity (DST = 0.04). The allelic richness of the progeny ranges from 2.07 to 3.13. The NJM x GVT progenies are molecularly different from the control PB121+. In sum, 63.95% of the alleles present in the NJM x GVT progenies are absent in the BP121+ control. Furthermore, 8.14% of the alleles present in the control are absent in the NJM x GVT hybrids. Collecting samples for further work such as QTLs identification could take these results into account. Thus, it would be wise and advantageous to sample a high number of trees per progeny than to choose several families of progenies. The allelic richness of the progenies could guide the choice of progenies. The markers comprising the private alleles detected between the PB121+ and NJM x GVT progenies can be used in the varietal purity tests.