Abstract Macrobrachium rosenbergii nodavirus ( Mr NV) is a pathogen of freshwater prawns that poses a threat to food-security and causes significant economic losses in the aquaculture industries of many developing nations. A detailed understanding of the Mr NV virion structure will inform the development of strategies to control outbreaks. The Mr NV capsid has also been engineered to display heterologous antigens, thus knowledge of its atomic resolution structure will benefit efforts to develop tools based on this platform. Here we present an atomic-resolution model of the Mr NV capsid protein, calculated by cryogenic electron microscopy (cryoEM) of Mr NV virus-like particles (VLPs) produced in insect cells, and three-dimensional image reconstruction at 3.3 Å resolution. CryoEM of Mr NV virions purified from infected freshwater prawn post-larvae yielded a 6.6 Å resolution structure confirming the biological relevance of the VLP structure. Our data revealed that unlike other known nodaviruses structures, which have been shown to assemble capsids having trimeric spikes, Mr NV assembles a T=3 capsid with dimeric spikes. We also found a number of surprising similarities between the Mr NV capsid structure and that of the Tombusviridae . 1. An extensive network of N-terminal arms lines the capsid interior forming long-range interactions to lace together asymmetric units. 2. The capsid shell is stabilised by three pairs of Ca 2+ ions in each asymmetric unit. 3. The protruding spike domain exhibits a very similar fold to that seen in the spikes of the tombusviruses. These structural similarities raise questions concerning the correct taxonomic classification of Mr NV.