Whole-genome sequence analysis has revealed that diatoms contain genes and pathways that are novel in photosynthetic eukaryotes. More generally, the unique evolutionary footprint of the chromalveolates, which includes a genome fusion between a heterotrophic protist and a red alga in addition to a major prokaryotic influence, has fostered their inheritance of a unique complement of metabolic capabilities. Many aspects of nitrogen metabolism and cell signaling appear to be linked in diatoms. This new perspective provides a basis for understanding the ecological dominance of diatoms in contemporary oceans.