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The classification of Eriosyce subgenus Neoporteria ("subsection" in the sense of Kattermann) and the role of allopatry/sympatry in the diversification of the group were studied by use of cladistic and predictive distribution modeling methods. We reconstructed the phylogenetic relationships of subgenus Neoporteria by analyzing 38 morphological characters and DNA sequences from two chloroplast regions of 21 taxa from the Chilean subsections of Eriosyce using a Bayesian and maximum likelihood phylogenetic framework. Also, we attempted to find out if the divergence between the sister taxa in the Neoporteria group had been caused by allopatric or sympatric mechanisms. The morphology-based analysis placed E. chilensis basal within the Neoporteria clade and suggested a further broadening of the group by including E. taltalensis var. taltalensis, formerly considered a member of subsection Horridocactus. However, the combined DNA data placed E. sociabilis and E. taltalensis var. taltalensis within the Horridocactus clade, and placed E. chilensis with E. subgibbosa var. litoralis. The broad concept of E. subgibbosa sensu Kattermann (comprising seven infraspecific taxa), was rejected by our combined molecular results. Finally, our results corroborated changes in subsection Neoporteria proposed by various authors and suggested further modifications within Neoporteria. The analyses of the degree of geographic overlap of the predicted distributions indicated null overlap between the sister taxa, and one probable hybrid origin of E. chilensis, indicating that evolutionary divergence is mainly caused by an allopatric process associated with climatic tolerance.