Pogogyne (Lamiaceae) is a small genus of annual plants, occurring almost entirely in vernal pool habitats. To infer the phylogenetic relationships of this group, DNA sequence data from the trnQ-rps16 chloroplast spacer and both ETS and ITS nuclear regions were obtained from all seven extant species and several outgroups and analyzed using both parsimony and Bayesian phylogeny reconstruction methods. Ancestral state reconstructions were performed for morphological characters that have been used to separate groups within Pogogyne. This study indicates that subgenus Hedeomoides is monophyletic with good support and can be diagnosed by two apomorphies: a reduction in stamen number and a reduced corolla size. Subgenus Pogogyne is paraphyletic, but with poor support. Several clades within the genus Pogogyne have discrete biogeographic distributions. The Pogogyne genus clade has a relatively long stem lineage, but its crown clade has quite short branches. Our estimate for the mean divergence time of the stem node is 5.1–7.7 million years ago and for that of the crown node is 0.9–1.9 million years ago, the latter overlapping with ages of vernal pool ecosystems. These results support the hypothesis that the members of Pogogyne underwent a rapid diversification in response to specialization to a periodically inundated habitat.