Comparative genomics is a powerful approach to illuminate the genetic basis of phenotypic diversity across macro-evolutionary timescales. Recent advances in sequencing, genome assembly, annotation, and comparative methods promoted large-scale analyses that unveiled genomic determinants contributing to differences in cognition, metabolism, and body plans as well as phenotypes with biomedical relevance, such as cancer resistance, longevity, and viral tolerance. These studies highlight joint contributions of multiple molecular mechanisms and indicate an underappreciated role for gene and enhancer losses driving phenotypic change. However, challenges remain, including comprehensive phenotype databases and genome annotations, improved approaches for identifying lineage-specific adaptations, and functional tests. Here, we review recent progress, highlight major discoveries, and discuss future directions for linking phenotype to genotype using comparative genomics.