The advent of the polymerase chain reaction (PCR) and DNA sequencing nearly 20 years ago revolutionized our fundamental understanding of algal evolution. Today, we sit at the beginning of a new era of comparative phylo-genomics, an area in which algae will play a central role in elucidating the network of life. In this review we tour the original “morphology vs. molecules” debate, the renewed role of ultrastructure, the discovery of cryptic species and the many paraphyletic taxa that pervade virtually all lineages of algae, evaluate molecular clocks, and discuss what to make of the new DNA barcoding. Full integration of taxonomy, phylogenetics, classification, and nomenclature under the systematics umbrella is more cogent than ever as losses of biodiversity continue to increase and the role of herbarium collections and databases becomes ever more important in assessing the relationship between biodiversity and ecosystem function over all scales. We round out our review with a look into the new field of genomics that will take the revolution to the deepest and shortest internodes, to the paraphyletic tips of species and populations. Use of many concatenated genes and resequencing technologies are already here, thus opening new possibilities to understand the very process of speciation through adaptive population divergence. The 21st century systematist will be cross-trained as a molecular naturalist including knowledge of bioinformatics.