The brown algae are one of the largest and most important groups of primary producers in benthic coastal marine environments. Despite their biological importance, consensus regarding their taxonomic or evolutionary relationships remains elusive. Our goal was to produce a taxon-rich two-gene (rbcL and LSU rDNA) phylogeny. Key species were sequenced to represent each order and family in the analyses across all 19 orders and ∼40 families, including selected outgroups Schizocladiophyceae and Xanthophyceae. Our results are in sharp contrast to traditional phylogenetic concepts; the Ectocarpales are not an early diverging clade, nor do the Fucales diverge early from other brown algae. Rather, Choristocarpus is sister to the remaining brown algae. Other groups traditionally considered to have primitive features are actually recently diverged lineages, turning traditional phylogenetic concepts upside down. Additionally, our results allow for the assessment, in the broadest context, of many of the historical and more recent taxonomic changes, resulting in several emended groups along with proposals for two new orders (Onslowiales, Nemodermatales) and one new family (Phaeosiphoniellaceae).