Little is known about the amount and spatial distribution of diversity within and among deadwood-dependent insect species and saproxylic communities as a whole. Molecular approaches offer a solution to these knowledge gaps, even in cases where species and genera are not yet formally described. Indeed, molecular data are broadly connectable among otherwise unrelated studies and directly complement the invaluable work of expert taxonomists. Here we provide an overview of the applications of molecular tools for assessing saproxylic insect diversity. To do this, we use an organizational framework based on the hierarchy of biological units, beginning with diversity at the intraspecific level, followed by species-level diversity within genera, and then close with community-level diversity. Within each of these sections, we consider the types of genetic data that have typically been used and provide an overview of research questions and findings from the primary literature.