Probe sets have been designed to broadly target gymnosperms, angiosperms, or specific plant families (i.e., Asteraceae, Fabaceae, Ochnaceae, etc.), enabling great advances in our understanding of evolutionary relationships in large plant groups. The Asteraceae specific probe set, Compositae-1061, has become popular among researchers studying members of Asteraceae, and has helped pave the way for investigations at lower taxonomic levels and non-model organisms. Though Compositae-1061 has shown to be highly efficient at higher- and some lower-taxonomic levels within the family, it generally lacks resolution at the genus to species level. In this study, we collected 48 transcriptomes spanning Asterales to generate an improved probe set designed specifically for Asteraceae using the software MarkerMiner. Using this new probe set, we sequenced 17 Packera Á. Löve & D. Löve and two outgroup Senecioneae taxa that have previously been sequenced using the Compositae-1061 probe set. Sequences from both probe sets were then used to generate phylogenetic trees, compare their topologies, and assess node support to determine whether this new probe set provided greater resolution at the genus/species level compared to Compositae-1061. We found that the newer probe set recovered drastically less paralogous sequences than Compositae-1061, with only about 5% of the recovered loci reporting as paralogous with the new probe set, and 59% with the 1061 probe set. Additionally, we found that discordance was lower and species relationships more closely followed previous studies when utilizing the new probe set. Alternatively, we found that Compositae-1061 produced less missing data and was more parsimony informative than the newly designed probe set. We anticipate that further testing will provide additional support for the utility of this probe set in complex groups in the sunflower family.