The Opuntia genus includes over 181 species comprising, on the basis of morphological traits, a total of 29 series [The Cactaceae(1919)]. Starting from this classification, several authors have investigated the Opuntia genus taxonomy but the large morphologicalvariation within different species, suggests that phenotypical characteristics will not serve to produce a stable classification. In thiswork chloroplastic simple sequence repeat (cpSSR) and amplified fragment length polymorphism (AFLP) were used to evaluate theusefulness of molecular markers in Opuntia species characterization and to study the relationships among different species. Resultsshow that the combination of cpSSR and AFLP markers provide a quantitative estimation of genetic relationships among severalOpuntia species. Both molecular analyses reveal a genetic similarity among species of series 20 and 21 [The Cactaceae (1919)] assuggested also by morphological traits. Particular attention was focused on the genetic relationship between Opuntia ficus-indica andOpuntia megacantha: individuals from different populations of the two species were analyzed with both molecular markers. Acommon genetic constitution of O. ficus-indica and O. megacantha was detected. On the basis of molecular data, morphologicaltraits and biogeographical distribution, we suggest that O. ficus-indica should be considered as a domesticated form of O.megacantha. Our results suggest the importance of a revision of Opuntia genus classification using several tools: molecular,morphological and biogeographical analysis.

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