Target enrichment of highly conserved, phylogenetically informative loci has helped reconstruct and study the evolutionary history of organismal groups ranging from cnidaria and arthropods to major vertebrate clades such as birds and snakes. Among fishes, researchers have designed enrichment bait sets that can collect data from hundreds of loci shared among a majority of ray-finned fishes (Actinopterygii 33,444 species) or more than one thousand loci shared among actinopterygian sub-clades like the acanthomorphs, the group of spiny-finned fishes that dominates the world’s oceans. However, no target enrichment bait set exists that is tailored to collect sequence data from conserved loci shared by ostariophysan fishes, which constitute the second largest actinopterygian superorder (Ostariophysi 10,887 species). Here, we describe the design of an enrichment bait set that targets 2,708 conserved, nuclear loci shared among ostariophysan fishes, and we empirically demonstrate how sequence data collected using this bait set can resolve phylogenetic relationships at several levels of divergence across the ostariophysan tree of life.