A phylogeny of the diatoms (Bacillariophyta) has been inferred from nuclear-encoded small subunit ribosomal RNA (rRNA) sequence analyses of 30 taxa in 11 orders. Maximum likelihood, weighted maximum parsimony, neighbour-joining, and Log-Det transformation methods each recover two clades, neither of which correspond to the classes of diatoms presently recognized; Class Coscinodiscophyceae (centric diatoms). Class Fragilariophyceae (araphid pennate diatoms) and Class Bacillariphyceae (raphid pennate diatoms). Nor do the clades correspond to the traditionally recognized centric and pennate diatoms. One clade is defined by the centric diatom orders Coscinodiscales, Rhizosoleniales, Corethrales, and Melosirales. The second clade contains the bi- (multi) polar centric diatoms, the centric diatoms with strutted processes, and the pennate diatoms. Tests of alternative phylogenies under maximum likelihood strongly support these divergences. Fossil evidence from the earliest best-preserved diatom deposit (115-110 Ma ago, Ocean Drilling Program (ODP) Leg 113, Site 693, Antarctica) also suggests that these divergences in the diatoms occurred early in their evolution and are correlated taxonomically with the absence (clade one) or presence (clade two) of a central tube in the silica cell wall. Its presence can be traced to the central tube or labiate process in the bipolar centric taxa, to the central tube or strutted process in the order Thalassiosirales and probably to the organelle that evolved into the raphe of the pennate diatoms. Divergence times place the origin of the diatoms around 300 Ma ago (Carboniferous).