Heterokont algae are a large and diverse monophyletic group. This "crown" taxon of morphologically diverse organisms evolved about 300 million years ago and radiated after the Cretaceous period. Members of this assemblage vary in morphology from simple unicells to highly complex, parenchymous seaweeds with intricate reproductive structures. Their closest relatives are the nonphotosynthetic aquatic pseudofungi, plant pathogens (mold and mildew pseudofungi), and various protozoan flagellates. The importance of heterokont algae is not always apparent to terrestrially-focused scientists. This group of algae is indispensable to global ecosystem health. Autotrophic members serve as the penultimate anchor of the ocean food web and process almost half of the carbon fixed on earth. At present, 14 classes of photosynthetic heterokonts are recognized, encompassing between 100,000 and one million species. The GOAL of this proposal is to determine the phylogenetic relationships among the heterokont classes, which remarkably remain unresolved despite two centuries of light microscopic study, 50 years of electron microscopic study, and 20 years of molecular investigations. Two large molecular data sets will be generated to accomplish this goal: (1) DNA sequences of seven nuclear, mitochondrial, and plastid genes from 300+ heterokont algal species; and (2) entire chloroplast genome sequences from 20+ species of heterokont algae. We have assembled a team with expertise in heterokont algal systematists, phylogenetic analysis, and chloroplast genomics to tackle this problem. External collaborators on this project include additional heterokont systematists, molecular and evolutionary biologists, and phylogeneticists. Our combined expertise and intensive molecular investigation will resolve the phylogenetic relationships for one of largest and most neglected groups of photosynthetic organisms in the Tree Of Life.