Litchi (Litchi chinensis Sonn.) is a fruit crop with a clear niche for expansion in countries with subtropical climates. One of the main limitations for breeding purposes and optimum germplasm management in this species is the confusion in cultivar denomination among different producing countries and germplasm collections worldwide. Litchi cultivar identification is still mainly based on morphological characters, and homonymies and synonymies are very frequent. To address this gap, a molecular study was conducted to characterize litchi accessions from two of the main litchiproducing regions for the export market, Mauritius and Réunion, and to compare them to those obtained from litchi cultivars from different origins conserved in a germplasm collection in Spain. Eleven simple sequence repeat (SSR) loci were used to characterize molecular polymorphisms among 88 litchi accessions conserved in Mauritius, Réunion, and Spain. A total of 67 amplification fragments were detected with those 11 SSRs, with an average of 6.1 bands/SSR. Three primer pairs seemed to amplify more than one locus. The mean expected and observed heterozygosities over the eight single locus SSRs averaged 0.53 and 0.61, respectively. The total value for the probability of identity was 9.78×10?4. Molecular characterization revealed the existence of 42 different genetic profiles. Several synonymies and homonymies in litchi cultivar nomenclature both within and across geographical regions were found. This comparative study provides the basis for the standardization of litchi cultivar nomenclature over the studied regions and in other litchi-producing countries.