Much attention is being directed toward understanding and co-opting the mechanisms by which diatoms control patterning of silica for nanotechnology applications. Given the enormous diversity of cell-wall patterns among diatom taxa, a complete understanding of these mechanisms will require comparative analysis of nanopatterning strategies from a diversity of diatom taxa. A well-supported phylogenetic tree provides the best basis for such comparisons because closely related taxa will have many similar attributes (morphological, physiological, ecological, etc.) simply because they share a recent common ancestor. Phylogenetic information is exploited in as diverse a set of fields as pharmacology, epidemiology, and geology. Nanotechnologists can use the phylogenetic tree of diatoms to help select exemplar taxa and to streamline the search for alternative nanopatterning strategies. We review the progress made thus far in reconstructing the phylogeny of diatoms. Most analyses have been based on small subunit ribosomal DNA sequences, and inferences have varied substantially depending on the number and diversity of taxa included in the analyses. We review several seminal studies on diatom phylogeny in light of theoretical and empirical investigations that have emphasized the critical importance of taxonomic sampling on phylogenetic inference. One consistent result is that centric diatoms grade into araphid pennates, and araphid pennates grade the raphe-bearing pennate diatoms, which are a natural group. Including more taxa and more characters (molecular and morphological) should yield a better supported hypothesis of diatom relationships.