The degree of systematic resolution across the teleost tree of life has increased exponentially since the introduction of phylogenetic methods in the 1970s as a mean to resolve evolutionary histories. With advances in sequencing technologies, the leap from genetics to genomics has been equally rapid. However, despite numerous well-supported phylogenetic reconstructions, many nodes in the fish tree of life have remained a challenge to resolve. Factors underlaying the astonishing diversity of teleosts, particularly across taxonomically broad assemblages such as fishes associated with tropical reefs, have intrigued evolutionary biologists for decades. Identifying and understanding the implications of those factors require comprehensive genetic material and robust phylogenetic frameworks. In this presentation, I will introduce some of the recent advances in next-generation sequencing and discuss how genomics are impacting the taxonomy and our understanding of reef fish’s evolutionary histories.