Fifty-six accessions involving five taxa of Nephelium (N. Iappaceum varieties lappaceum and pallens, N. hypoleucum, N. ramboutan-ake, and N. cuspidatum) were fingerprinted and evaluated for genetic diversity using isozyme polymorphism. All five taxa were polymorphic for most of the enzymes encoded by 10 putative loci. Number of alleles per locus ranged from three for Pgi-1 to nine for Pgi-2 with a total of 57 alleles. Thirty-eight accessions out of 56 possessed unique isozyme genotypes, indicating a high level of diversity in the collection. On average, 80% of the loci were polymorphic and the expected and observed heterozygosities were 0.374 and 0.373, respectively. The cluster analysis of the isozyme data revealed five distinct clusters representing the five taxa included in the study. Genetic differentiation within N. Iappaceum var. Iappaceum was evident from the cluster analysis. Isozyme data indicated that N. ramboutan-ake is the closest relative of N. Iappaceum var. Iappaceum, followed by N. hypoleucum, N. Iappaceum var. pallens, and N. cuspidatum. Interestingly, the varieties of N. Iappaceum exhibited genetic divergence far beyond that of the congenerics, N. hypoleucum and N. ramboutan-ake and may require a taxonomic revision.