Phylogenetic studies conducted with two nuclear ribosomal markers created the first phylogenetic framework in which to understand evolutionary relationships in Mentzelia section Bartonia (Loasaceae), but low molecular variation resulted in several large polytomies and an incomplete understanding of species relationships. We applied a genome skimming approach to determine whether additional genetic variation generated from high-throughput sequencing could resolve relationships in one of the largest polytomies in the section. Among the 20 species sequenced, five species that have pinnatisect leaf morphology were previously hypothesized to be monophyletic and we tested whether additional data would resolve the group as monophyletic. For the chloroplast genome, reads were assembled with de novo and reference guided approaches, whereas reference guided approaches were taken for the nuclear ribosomal cistron region and a single anonymous nuclear locus. Significant discordance was identified among all three gene trees. Exhaustive measures were taken to ensure phylogenetic and assembly-based errors were not responsible for the observed discordance among gene trees. We attribute incongruence to a low phylogenetic signal to noise ratio that is likely caused by the clade radiating recently and rapidly and perhaps unique evolutionary histories among genomes. Despite incongruence, several well-supported relationships emerged across data sets, and although two out of three gene trees did not recover a monophyletic pinnatisect group, all hypothesis tests for a monophyletic pinnatisect group among gene trees failed to reject monophyly of the group.