The genus Pogogyne is a member of the mint family, Lamiaceae, a very diverse clade of angiosperms. Recent phylogenetic research recovers Pogogyne in the sub-tribe Menthinae, tribe Mentheae, of subfamily Nepetoideae. Previous research suggested that Pogogyne underwent a relatively rapid diversification following their adaptation to vernal pool or “temporary wetland” conditions 0.9–1.9 mya. In this study, Pogogyne is used as a model for the phylogenomic study of rapid divergence within closely related taxa. To accomplish this, two high throughput sequencing technologies are compared: 1) a method utilizing Illumina technology to sequence the high copy organellar fraction of genomic DNA, termed ‘genome skimming,’ and 2) a method that relies on Illumina sequencing of an enzyme catalyzed reduced sample of genomic DNA, known as restriction-site associated DNA sequencing (RADseq). Both types of data were analyzed using maximum likelihood and Bayesian algorithms. The analyses of both types of data were similar to previous findings, but the new data inferred topologies with much higher support than those that were obtained from earlier studies. Results support a monophyletic genus Pogogyne, a monophyletic subgenus Hedeomoides, and the suggestion that two novel species exist in the genus.