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Despite efforts for a complete phylogeny of Cactaceae, generic circumscription and species level relationships remain unsolved. Within Astrophytum one species is assigned to a different genus (Digitostigma) and two are often treated as a single species (A. myriostigma and A. coahuilense). Astrophytum is endemic to the Chihuahuan Desert, but may also be found in adjacent regions. We reconstructed the phylogeny to date the origin of Glades and infer the biogeographic patterns of Astrophytum in order to understand the relationships between group members. Three sequences of chloroplast DNA (rbcL gene, trreL-trnF intergenic spacer, and trnK-matK region) were used with Bayesian and Maximum likelihood methods to generate a phylogeny. Divergence times for each node were estimated using an uncorrelated lognormal clock (BEAST) and inferred ancestral distribution using RASP. Astrophytum is monophyletic, with six species grouped in two main clades. Astrophytum caput-medusae (recognized as Digitostigma) is derived within Astrophytum. Individuals of A. myriostigma and A. coahuilense are grouped in independent clades, supporting their recognition as distinct species. Data suggest posterior diversification in the Late Miocene, during a transition to drier climates in North America. Occurrences of Astrophytum species outside of the Chihuahuan Desert are attributable to two recent independent events.