Since the sudden burst of Angiosperms in the Mid-Cretaceous, flowering plants have steadily diversified while continually evolving new and innovative structures. Staminodes are infertile stamens that are sometimes functionally co-opted to perform novel functions other than pollen production, including a variety of supportive roles in pollination or protection. Petaloid staminodes, such as those found in Mentzelia section Bartonia (Loasaceae, Cornales), for example, are likely co-opted for pollinator attraction. Mentzelia section Bartonia has emerged as a recent and rapidly evolving clade of 51 species that are distributed across western United States and northern Mexico. Approximately half of the species contain staminodes, but a fully resolved phylogeny is needed to identify the number of times staminodes have been gained or lost. Because of its recent and rapid evolution, reconstructing a fully resolved phylogeny has been hampered by low sequence divergence, high cytonuclear discordance, and cryptic morphological changes, which have impeded phylogenetic reconstruction using a limited number of plastid and nuclear markers. To better infer species relationships, we implemented a target-capture approach with the Angiosperms-353 nuclear bait set for all taxa in the section. Sequences for orthologous supercontigs (combined intron and exon regions) were assembled with HybPiper and maximum likelihood gene trees were reconstructed in 1,000 bootstrap replicates and compiled into a species tree using Astral-III. The chloroplast genome was also sequenced with genome skimming and a phylogeny was reconstructed with maximum likelihood. We discuss species relationships within the section, compare phylogenies reconstructed with Angiosperms-353 baits to those inferred with chloroplast genomes, and examine how many times staminodes have been gained and lost in the group.