Objective: Mezcal agaves in the state of Oaxaca have a high economic value due to the demand for mezcal production; therefore, the purpose of this work was to assess and highlight the importance of morphological diversity within and among cultivated Agave species. Design/Methodology/Approach: A completely randomized experimental design with 25 treatments (populations) and 11 replicates (individuals) was implemented. The plant (individual) was the experimental unit and 19 morphological descriptors proposed by the National Seed Inspection and Certification Service (SNICS) were assessed. A total of 275 individuals of the Agave angustifolia, Agave karwinskii, Agave marmorata, Agave rhodacantha, Agave potatorum, Agave seemanniana, and Agave nussaviorum species were assessed using a multivariate analysis to determine their phenotypic variability and existing relationships. Results: The dendrograms for the Q-mode and R-mode were obtained by means of a cluster analysis, forming 4 groups based on the average linkage generated from the standardized BDM of the sampled species of the genus Agave. Four groups were formed using the k-means clustering method, in accordance with field observations and a review of the taxonomic bibliography. The first two principal components (PC) accounted for 66.4% of the total variation, according to the principal component analysis (PCA). For PC1 and PC2, the variables with the highest contribution were those related to leaf shape (Fh), size of the lateral spine (FEL), number of leaves (Nh), plant height (H), uniformity in the size of the lateral spines (UTE), and terminal spine shape (FET). Study Limitations/Implications: A comprehensive study requires taxonomic keys to identify species, subspecies, and even varieties of Agave. Additionally, molecular characterization is essential to understand the variability and phylogenetic relationships of these populations, subject to a phylogenetic analysis. Findings/Conclusions: Multivariate analysis techniques revealed that three species showed high phenotypic variability in the maturation stage under cultivation conditions. The A. potatorum and A. karwinskii species had a greater intra-population phenotypic variability, with significant differences within the same species. Agave marmorata showed no intra- or inter-population variability. Leaf texture (Txh) was the only variable that explained the variation within its group. This is a tall species whose diameter is larger than in the other species. The variables of the Mexican (Agave rhodacantha) group showed low correlation, as their behavior was highly dispersed. The variables obtained in the field from this group of populations must be meticulously assessed to identify the degree of correlation between the variables and to confirm the behavior of this group.