Mussels of order Unionida are a group of strictly freshwater bivalves with nearly 1,000 described species, with a dispersed geographic distribution across the world’s freshwater ecosystems. Despite their fundamental ecological importance, they are highly threatened, being the faunal group with the highest records of wild extinctions. To date, only five freshwater mussel species have had their whole genome sequenced, of which only two are from European species. Here, we present the first genome assembly of the painter’s mussel, Unio pictorum (Linnaeus, 1758), the type species representative of the order and the most widespread species of the genus in Europe. We used long-read PacBio HiFi sequencing reads to produce a highly contiguous assembly that will pave the way for the study of European freshwater mussels in the Genome Era.