How is organismal biology changing in the era of genomics? Here, I discuss one example, the changes and trends in the systematics of reptiles and amphibians. The polymerase chain reaction, automated sequencing, and genomic tools now make it possible to apply a vast number of molecular characters to questions of phylogeny and species limits. At higher taxonomic levels, recent studies using these data have revealed some unexpected relationships, but also strong support for many traditionally recognized groups. At lower levels, molecular studies suggest that numerous species have been hidden by misleading taxonomy and morphological conservatism. However, the computational tools for analyzing multilocus data for phylogenetics and species delimitation are in need of further development, including greater integration with population genetics. Given current trends, much of reptile and amphibian phylogeny may soon be resolved. Although opportunities for tree-making by future systematists may shrink, opportunities for using phylogenies to address evolutionary and ecological questions should blossom.