Objective: To physically and chemically characterize clonal selections of Persian lime(Citrus x latifolia Tanaka ex Q. Jiménez).Design/Methodology/Approach: The principal components analysis was employed,using a mixed data factorial analysis model. Genotype distribution was graphed usingprincipal components with the k-medoids method, while a Gower’s dissimilarity matrixwas determined for the conglomerate analysis and a dendrogram was developed usingWard’s minimum variance cluster method. For the morphological characterization of thefruits, the study considered the following trees: Citrus volkameriana, Citrus macrophylla,Citrus paradisi X Poncirus trifoliata, X Citroncirus spp., and Citrus X aurantium. Thefruit’s diameter, length, weight, color, and shape were analyzed, in addition to its baseshape, tip shape, surface texture, albedo adherence, number of seeds, ripening rate,juice weight, juice yield, pH, °Brix, and titratable acidity. Data were analyzed using Rsoftware and the factoextra and FactoMineR packages.Results: The physical and chemical traits of Persian lime fruit vary due to thecorrelations between the types of rootstock that are cultivated in the citrus zone studied. Study Limitations/Implications: Farmers do not know which clone or type of plantmaterial they propagate; they simply select clones that show outstanding morpho-agronomical traits.Findings/Conclusions: The morphological diversity and quality of the fruit is related tothe type of rootstock used in its propagation, in addition to internal and external traits inCitrus macrophylla standing out in fruit quality.