Opuntia is a genus of plants known as prickly pear cactus (nopales), with about 200 species, and is taxonomically complicated. The present study was focused on characterizing micromorphology and providing a phylogenetic hypothesis to place Opuntia setocarpa (described in 2017) in relation to other related species. Three individuals were characterized and collected in Neverías in the Sierra of Cacoma of the municipality Autlán de Navarro in Jalisco, Mexico. The micromorphology of spines, epidermis and stoma was characterized with scanning electron microscopy. The phylogenetic hypothesis was performed with maximum likelihood and Bayesian Inference including other Mexican species. Opuntia setocarpa is recovered as a supported species within Opuntia s.s.