ABSTRACT. – Phylogenies of the diatoms have largely been inferred from SSU rDNA sequences. Because previously published SSU rDNA topologies of araphid pennate diatoms have varied, a supertree was constructed in order to summarize those trees and used to guide further analyses where problems arose. As previously seen with the SSU trees, araphid diatoms were divided into two clades: basal and core araphids. The basal clade is sister to a clade containing other araphids (core) and the raphid diatoms. Several subclades recovered in the supertree did not correspond to current taxonomy in the diatoms but were supported by ecological and/or morphological characters. A phylogeny of diatoms was then estimated using four gene markers, SSU and LSU rDNA, rbcL and psbA (total 4352 bp) with 42 diatom species chosen to resolve problems in the supertree. Two rooting strategies were explored: 1) one bolidomonad as the closest outgroup of the diatoms and, 2) one bolidomonad and more distantly related heterokontophyte outgroups. Two different strategies were employed to analyze the four gene tree with both Maximum Likelihood (ML) and Baysian Inference (BI) methods. In the first strategy, the variable regions of the LSU rDNA and the third codon position of rbcL were recoded into R (A+G) and Y (T+C) because of substitution saturation detected at these positions in these genes. In the second, these regions were not recoded. Tree topologies of pennates were nearly identical in all analyses. Pennates were divided into three major clades, basal araphid, core araphid and raphid diatoms, as shown in the supertree. The four gene trees displayed better resolution and had stronger bootstrap within the subclades than those of the SSU supertree. The divergence time of the pennates with a Bayesian estimation was estimated, allowing for simultaneous constraints from the fossil record and varying rates of molecular evolution of different branches in the phylogenetic tree. The radiation of pennates into three major clades took place in a short period of geological time before their first appearance in the fossil record and earlier than that proposed by other clocks using single genes.