In this study, qualitative morphological characters, traditional and derived morphometric descriptors, palynological traits, and multivariate analyses were integrated to evaluate morphological variation among five wild and cultivated Opuntia taxa from the coastal region of La Libertad, Peru, including a morphotype of Opuntia ficus-indica. Vegetative characters revealed differences in cladode architecture, spine development, and growth habit, whereas derived morphometric descriptors improved the characterization of shape and the relative arrangement of morphological structures. Floral, fruit, seed, and pollen characters showed consistent differences among the evaluated taxa that were further supported by principal component analyses, suggesting patterns of morphological variation. The morphotype of O. ficus-indica showed consistent morphological differentiation from cultivated O. ficus-indica within the sampled material, particularly in reproductive traits, cladode architecture, and spine development. Overall, the integration of macro and micromorphological evidence with derived morphometric descriptors provided a comprehensive characterization of phenotypic variation and represents a useful approach for documenting morphological differentiation within Opuntia. Further integrative studies are needed to clarify the taxonomic significance of this morphological differentiation.