The Cretaceous-Paleogene (K-Pg) mass extinction has been linked to explosive diversification across major clades of terrestrial vertebrates. The impact of the K-Pg event on diversification of marine vertebrates is less clear. Although the fossil diversity of the Acanthomorpha (spiny-rayed fishes), the dominant clade of marine fishes, increases sharply during the Paleocene, molecular timescales suggest a decoupling between the K-Pg event and the rise of modern acathomorphs. Outstanding questions concerning the phylogenetic relationships of acanthomorphs confound efforts to understand the impacts of the K-Pg on modern fish diversity. The overwhelming species richness (>18,140 species) and astonishing phenotypic diversity of this clade present a serious challenge to morphological and molecular phylogenetics, with uncertainty spanning both the placement of early diverging lineages and the resolution of enormously diverse subclades like the infamous percomorph "bush at the top of the tree". Recent multi-locus studies offer phylogenetic hypotheses for acanthomorphs that suggest a number of newly discovered lineages. However these new relationships and associated timescales have yet to be interrogated by phylogenomic approaches. Here, we use targeted enrichment of more than 1,000 ultraconserved elements (UCEs) comprising > 300,000 nucleotide positions in conjunction with a divergence time analysis based upon a novel set of fossil calibrations to resolve relationships among 120 major acanthomorph lineages and provide a new timescale for this radiation. Maximum likelihood, Bayesian, and species tree analyses result in a well-supported topology that strongly resolves relationships along the acanthomorph backbone and reveals new relationships within six major percomorph subclades. Divergence time analyses reveal a pulse of diversification within each major percomorph lineages that coincides with the K-Pg boundary. Our results align molecular phylogenetic studies with recent paleontological analyses and reveal the K-Pg as a major event contributing to the present day dominance of marine and terrestrial vertebrate lineages.