This Special Issue celebrates viruses of microbes: those viruses that infect archaea, bacteria and microbial eukaryotes. This issue is associated with the 6th Viruses of Microbes (VoM) conference in Guimarães (www.vom2020.org, accessed on 1 April 2021), Portugal, that was originally planned for the summer of 2020, but has, in light of the pandemic, been postponed to 18–22 July 2022.