Type IV secretion systems (T4SSs) are large macromolecular machines that translocate protein and DNA and are involved in the pathogenesis of multiple human diseases. Here, using electron cryotomography (ECT), we report the in situ structure of the Dot/Icm type IVB secretion system (T4BSS) utilized by the human pathogen Legionella pneumophila. This is the first structure of a type IVB secretion system, and also the first structure of any T4SS in situ. While the Dot/Icm system shares almost no sequence similarity with type IVA secretion systems (T4ASSs), its overall structure is seen here to be remarkably similar to previously reported T4ASS structures (those encoded by the R388 plasmid in Escherichia coli and the cag pathogenicity island in Helicobacter pylori). This structural similarity suggests shared aspects of mechanism. However, compared to the negative‐stain reconstruction of the purified T4ASS from the R388 plasmid, the L. pneumophila Dot/Icm system is approximately twice as long and wide and exhibits several additional large densities, reflecting type‐specific elaborations and potentially better structural preservation in situ. Synopsis Bacterial type IV secretion systems translocate protein and DNA, and are involved in the pathogenesis of multiple human diseases. This study presents the in situ structure of the Dot/Icm type IVB secretion system from the human pathogen Legionella pneumophila. First structure of a type IVB secretion system, and also the first structure of any T4SS in situ. The Dot/Icm system shares almost no sequence similarity with type IVA secretion systems (T4ASSs). The basic architecture of the type IVB secretion system is however strikingly similar to the type IVA secretion system. Bacterial type IV secretion systems translocate protein and DNA, and are involved in the pathogenesis of multiple human diseases. This study presents the in situ structure of the Dot/Icm type IVB secretion system from the human pathogen Legionella pneumophila.