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The landscape of western North America has dramatically transformed since the Miocene to become increasingly heterogeneous, in turn promoting the evolution of many rapidly radiating angiosperm lineages. Phylogenetic relationships of these recently and rapidly radiating groups are difficult to resolve as there is little genetic variation among species and a high degree of noise from incomplete lineage sorting and hybridization. Mentzelia section Bartonia (51 species; Loasaceae) exemplifies this problem well. The clade has been investigated with Sanger sequencing, RADSeq, and genome skimming methods, however, most species relationships remain elusive due to low genetic variability. To better infer species relationships, we applied a hybrid enrichment approach with the Angiosperms353 probe set and implemented a novel bioinformatics workflow that aimed to maximize phylogenetic signal and minimize noise from low-quality sequences, paralogy, and incomplete lineage sorting. Our phylogenomic approach increased phylogenetic resolution of species relationships compared to previous studies based on nrDNA loci. Although a few species relationships still lack strong support, our results indicate that our methods were effective in phylogenetic inference of this recently and rapidly evolving lineage from western North America. To better characterize major groups in the Section, we propose the formal designation of three subsections: Decapetala, Multicaulis, and Multiflora.