A comprehensive phylogeny of ray-finned fish (Actinopterygii) and its molecular age estimates have been resolved using nine nuclear genes and 36 fossil calibrations. This study provides strong support for the phylogeny of all major ray-finned fish lineages and offers molecular age estimates consistent with the fossil record. The phylogeny resolves three key questions in teleost phylogeny: identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, offering a hypothesis on the radiation of early euteleosts, and providing a strategy for resolving the "bush at the top of the tree" that includes percomorphs and other spiny-finned teleosts. The study contrasts divergence time estimates from single nuclear genes or whole mitochondrial genomes, finding that the former underestimate the ages of the oldest ray-finned fish divergences, while the latter overestimate the ages of derived teleost lineages. The time-calibrated phylogeny reveals that much of the diversification leading to extant teleost groups occurred between the late Mesozoic and early Cenozoic, identifying this period as the "Second Age of Fishes." The study also highlights the importance of molecular data in resolving phylogenetic relationships and divergence times, which are critical for understanding the evolution and diversification of ray-finned fishes. The results show that the molecular age estimates are much closer to the fossil record than previously thought, suggesting that the fossil record may be incomplete for some lineages. The study provides a robust molecular framework for understanding the evolutionary history of ray-finned fishes and their diversification.A comprehensive phylogeny of ray-finned fish (Actinopterygii) and its molecular age estimates have been resolved using nine nuclear genes and 36 fossil calibrations. This study provides strong support for the phylogeny of all major ray-finned fish lineages and offers molecular age estimates consistent with the fossil record. The phylogeny resolves three key questions in teleost phylogeny: identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, offering a hypothesis on the radiation of early euteleosts, and providing a strategy for resolving the "bush at the top of the tree" that includes percomorphs and other spiny-finned teleosts. The study contrasts divergence time estimates from single nuclear genes or whole mitochondrial genomes, finding that the former underestimate the ages of the oldest ray-finned fish divergences, while the latter overestimate the ages of derived teleost lineages. The time-calibrated phylogeny reveals that much of the diversification leading to extant teleost groups occurred between the late Mesozoic and early Cenozoic, identifying this period as the "Second Age of Fishes." The study also highlights the importance of molecular data in resolving phylogenetic relationships and divergence times, which are critical for understanding the evolution and diversification of ray-finned fishes. The results show that the molecular age estimates are much closer to the fossil record than previously thought, suggesting that the fossil record may be incomplete for some lineages. The study provides a robust molecular framework for understanding the evolutionary history of ray-finned fishes and their diversification.