Abstract Nucleocytoplasmic large DNA viruses (NCLDVs) blur the line between viruses and cells. Melbournevirus (MelV, fam. Marseilleviridae ) belongs to a new family of NCLDVs. Here we present an electron cryo-microscopy structure of the MelV particle, with the largest known triangulation number (T=309) for a virus. The 230-nm particle is constructed by 3080 pseudo-hexagonal capsomers and encloses a membrane bilayer. Its most distinct feature is a large dense body (LDB) consistently found in all particles. Electron cryo-tomography of 147 particles showed that the LDB is located preferentially in proximity to the bilayer. The LDB is 30 nm in size and its density matches that of a genome/protein complex. More than 58 proteins are associated with the purified particle, including histone-like proteins, putative membrane proteins and capsid proteins. The observed intricate structural organization reinforces the genetic complexity of MelV, setting it apart from other viruses, and suggests an evolutionary link with cellular organisms.