A phylogeny of the diatoms was inferred from comparisons of nuclear-encoded small subunit ribosomal RNA coding regions using maximum likelihood, weighted maximum parsimony, and neighbor-joining distance methods with Jukes and Cantor, Kimura, Gamma, van de Peer, and LogDet evolutionary models. Analyses of 30 taxa in 11 orders recovered two clades (Clades I and II). Neither of these clades correspond to the three classes of diatoms presently recognized or to the traditionally recognized radially symmetrical centric diatoms or bilaterally symmetrical pennate diatoms. All analyses show that the centric diatoms are a paraphyletic lineage. Tests of alternative phylogenies that address existing hypotheses regarding diatom systematics with the maximum likelihood and maximum parsimony methods support the two clades. Clade I is defined by centric diatom orders with specialized tubes, termed labiate processes, located peripherally in the cell wall. Clade II contains (1) bi(multi)polar centric diatoms with centrally located labiate processes, (2) centric diatoms with other central tubes termed strutted processes, and (3) pennate diatoms. Morphological evidence from fossil assemblages and cytological architecture support the results of the molecular analyses, whereas morphological features of extant diatoms are too derived to resolve the deeper branches in the tree.