A phylogenetic analysis of all the intrageneric taxa of the genus Dioon Lindley (Zamiaceae) was undertaken by using chloroplast DNA restriction fragment length polymorphism analysis. Wagner parsimony analysis on a 187 character matrix yielded two equally parsimonious trees, differing only for the position of D. caputoi. The consensus tree has two well‐defined major clades. The first is composed of D. mejiae, D. rzedowskii, and D. spinulosum; the second is composed of D. califanoi, D. caputoi, D. edule var. angustifolium, D. edule var. edule, D. holmgrenii, D. merolae, D. purpusii, D. tomasellii var. sonorense, and D. tomasellii var. tomasellii. A phenetic analysis of the same data showed results broadly congruent with the cladistic analysis. This resulting phylogeny is partially congruent with morphological data and is also compatible with the biogeography of the genus. Modem species of Dioon may have evolved as a consequence of a very fast succession of vicariance events that mainly occurred during the early Cenozoic. The short time between each of these events may not have allowed the accumulation of a large number of morphological synapomorphies for the groups of species.