North American minnows of the Shiner Clade, within the family Leuciscidae, represent one of the most taxonomically complex clades of the order Cypriniformes due to the large number of taxa coupled with conserved morphologies. Species within this clade were moved between genera and subgenera until the community decided to lump many of the unclassified taxa with similar morphologies into one genus, Notropis , which has held up to 325 species. Despite phylogentic studies that began to re-elevate some genera merged into Notropis , such as Cyprinella , Luxilus , Lythrurus , and Pteronotropis , the large genus Notropis remained as a taxonomic repository for many shiners of uncertain placement. Recent molecular advances in sequencing technologies have provided the opportunity to re-examine the Shiner Clade using phylogenomic markers. Using a fish probe kit, we sequenced 90 specimens in 87 species representing 16 genera included in the Shiner Clade, with a resulting dataset of 1,004 loci and 286,455 base pairs. Despite the large dataset, only 32,349 bp (11.29%) were phylogenetically informative. In our maximum likelihood tree, 78% of nodes are 100% bootstrap supported demonstrating the utility of the phylogenomic markers at lower taxonomic levels. Unsurprisingly, species within Notropis as well as Hudsonius , Luxilus , and Alburnops are not resolved as monophyletic groups. Cyprinella is monophyletic if Cyprinella callistia is excluded, and Pteronotropis is monophyletic if it includes Hudsonius cummingsae . Taxonomic changes we propose are: restriction of species included in Alburnops and Notropis , elevation of the subgenus Hydrophlox , expansion of species included in Miniellus , movement of Hudsonius cummingsae to Pteronotropis , and resurrection of the genera Coccotis and Paranotropis . We additionally had two specimens of three species, Notropis atherinoides, Ericymba amplamala , and Pimephales vigilax and found signficant differences between the localities (1,086, 1,424, and 845 nucleotides respectively).