Pterocactus has 10 species endemic to restricted areas of the Argentine Monte and Patagonia regions, also growing in neighbouring Chile. We analysed phylogenetic relationships between its species, based on plastid DNA sequences (psbA‐trnH, rpl16, trnH‐matK), exomorphological features (spine type and size, stem segment form, flower position, epidermis colour, areole pubescence, stem surface) and cytogenetical traits (genome size, somatic chromosome number). Traits were mapped using character mapping and ancestral state reconstruction to understand the dynamics of evolutionary changes. Pterocactus was monophyletic. Two lineages were recovered: clade A (with P. fischeri diverging early and P. reticulatus, P. valentinii, P. megliolii, P. gonjianii, and both P. tuberosus forms) and clade B (with P. neuquensis diverging first and P. araucanus and P. hickenii). Both samples examined of P. australis were paraphyletic. It was estimated that Pterocactus split from its sister group at 9.38 mya. The crown group age was estimated to be 7.69 myr. Species showed x = 11 with different ploidy levels (2n = 22, 44, 99, ca. 110, and 154); only P. tuberosus f. tuberosus was diploid. The numbers were typical of each taxon studied, and polyploidy was important in its diversification. Two 18S‐5.8S‐26S sites were detected regardless of the ploidy level, except P. fischeri with four sites and 2n = ca. 110. The number of 5S sites was 2 in P. gonjianii and the diploid P. tuberosus f. tuberosus, 4 in the tetraploid P. tuberosus f. lelongii, 10 in the probably decaploid P. fischeri and 8 in P. araucanus of unknown chromosome number. The genome size ranged from 2C = 4.94 pg in P. megliolii of unknown chromosome number to 2C = 16.68 pg in the tetradecaploid P. hickenii. The ancestor is reconstructed as a dwarf shrub with cylindrical central spines of 16.35–31.2 mm long, non‐woolly areoles, cylindrical to globose/obpyriform stem segments, non‐tuberculate stem surface, lateral flower position, green/brown to violet epidermis, probably diploid, and with a genome size between 1.10 and 1.23 pg.