Phylogenetic relationships between and within Phacelia sections Whitlavia and Gymnobythus are inferred based on nuclear ribosomal DNA [5.8S, and flanking internal transcribed spacers (ITS) 1 and 2] and chloroplast DNA (rpl16 intron) sequences. These two sections share morphological characters and have been thought to be closely related. The purpose of this study is to test whether each of the two sections is monophyletic as well as whether they form sister clades. Our results indicate that section Gymnobythus is monophyletic, and members of section Whitlavia form two clades that correspond to subsections previously suggested by Gillett. In the ITS dataset, the two Whitlavia groups are not sister clades, but there is little support for their placement. The rpl16 and rpl16 ITS combined datasets provide resolution and strong support for monophyly of both sections. Both datasets indicate hybridization or a recent divergence between Phacelia parryi and Phacelia minor, as well as a close alliance between Phacelia longipes and Phacelia campanularia.