The systematics of Hydrophyllaceae (Boraginales) were investigated at three levels: a study of the pink-flowered and yellow-flowered plants in the genus Emmenanthe, an examination of the polyphyly of the genus Eucrypta, and molecular systematics of the taxa included in Phacelia sect. Ramosissimae. Pink-flowered Emmenanthe occurs in California in the Diablo Range and the Southern California mountains, and is occasionally sympatric with yellow-flowered Emmenanthe. Phylogenetic analyses of the internal transcribed spacer (ITS) region supported two reciprocally monophyletic evolutionary lineages corresponding to yellow-flowered and pink-flowered plants. Based on their evolutionary divergence and ability to remain distinct in sympatry, the two lineages in Emmenanthe are worthy of taxonomic recognition at the rank of species, as E. penduliflora and E. rosea (Brand) Constance, and are of evolutionary interest as examples of partially sympatric sister-species. Phylogenetic analyses of sequences from populations and specimens determined as Eucrypta chrysanthemifolia and E. micrantha, together with sequences representing major clades of tribe Hydrophylleae demonstrate that the two species in Eucrypta are not each other's closest relatives and represent disparate lineages in Hydrophyllaceae, confirming previous molecular studies. These results require recognition of a narrowed circumscription of Eucrypta sensu stricto (equivalent to E. chrysanthemifolia and varieties), a new genus, Vermisperma, and a new combination, Vermisperma micranthum, for E. micrantha. Evidence from the literature, museum specimen collections (databased and digitized), and molecular phylogenetic analyses were used in combination to revise the taxonomy of Phacelia sect. Ramosissimae (Rydb.) Walden & R.Patt.