Diatom ecology, physiology, and biotechnology research has been bolstered by the development of genetic engineering practices. The whole genome sequencing of two diatom species, Thalassiosira pseudonana and Phaeodactylum tricornutum, has greatly aided in shaping these into laboratory models by allowing researchers to characterize gene-expression and regulatory elements that are essential tools for synthetic biology and genetic engineering technologies. Tools that have been previously developed for other model organisms (yeasts, plants, animals), including gene overexpression, gene silencing, and targeted mutagenesis methods such as CRISPR-Cas9 have been quickly adapted for diatom research. Implementation of these tools relies on nucleic acid transformation methods to deliver the genetic payload to the diatom, be it particle bombardment or bacterial-mediated conjugation. Currently, more diatom species that may have alternative ecological relevance or attractive physiological or biochemical attributes in diatom biology, such as cold-adaptation or a benthic life-cycle are entering the genetic engineering fold. The breadth of molecular and genetic engineering tools employed in diatoms are reviewed here.