Cacti with the common name cholla are classified into several genera of the subfamily Opuntioideae (Cactaceae), and appear to be a monophyletic group. Although recent studies have provided strong resolution of the base of this group, assessment of evolutionary processes within genera have been limited due to taxon sampling. Analysis of four spacer and intron sequences of the chloroplast genome reveals evolutionary patterns and trends that are largely congruent with other recent studies. We concur with recent calls for the recognition of Micropuntia pulchella as monotypic and distinct from Grusonia, the name we use to refer to all species sometimes classified under Marenopuntia and Corynopuntia. Grusonia is monophyletic, and Cylindropuntia is borne on two clades of differing branch lengths. By incorporating the elements of ploidy, reproduction, and sequence divergence, we provide new insight into allopolyploid ancestry, the adaptive impact of ploidal-level variation in species, and the role of reproductive mode in diversification rates in the chollas.