With more than 24,000 extant species, the Actinopterygii is the most diverse group of vertebrates. This astonishing diversity represents not only an underexploited resource for research focused on these fishes but also a source of valuable information for comparative biology and medical science. Although the technical advances in morphology concomitant with revolutionary phylogenetic concepts have presented many challenges in ichthyology for the past half-century, spectacular progress in DNA technology provides other opportunities for research using multiple-gene or genomic data for the study of biological questions, particularly those related to the evolution of fishes. In this article, we discuss how ichthyology is changing in this new era, and how the emerging phylogenomic approach has been used to study species diversification in relation to gene and genome duplications and to resolve the complex evolutionary history of ray-finned fishes.