The Persian Lemon (Citrus latifolia) is an attractive species to Panamanian producers and investors. The Genetic Diversity of 16 Persian Lemon clones from two official nurseries; 11 of the Ministry of Agricultural Development (MIDA) and 5 of the Institute of Agricultural Innovation of Panama (IDIAP) was estimated using molecular markers Inter Simple Sequence Repeats (ISSR) in the Molecular Biology Laboratory of the Faculty of Agricultural Sciences of the University of Panama . 13 out of 17 evaluated ISSR primers were selected that generated 30 polymorphic bands. The PopGene® Computational Program was used to generate the results. The results reflected the existence of 3 duplicates among the 11 samples evaluated from Divisa and that 2 of the 5 samples from Rio Hato were also established in Divisa with different identifications. No duplicates were found within the Rio Hato samples. It is concluded the samples of Currency (1 and 4) (8 and 10) and (3 and 6) are the same genotypes. It was also possible to determine that the samples; Currency 9 and Rio Hato 13, although they have different identification, they are the same. Situation that is repeated with the samples Currency 11 and Rio Hato 12.