The zebra mussel, Dreissena polymorpha continues to spread from its native Ponto-Caspian range to lakes and rivers in Europe, the British Isles and North America. Despite the ecological and economic damage inflicted by this organism, there are currently few genomic resources for D. polymorpha, or related bivalves. Here we report the sequencing of the zebra mussel genome. Using a combination of long-read sequencing and Hi-C-based scaffolding, we generated a high-quality assembly with chromosome-scale scaffolds. We then used comparative analysis and RNA-Seq experiments to gain insights into adaptations that may underlie the ability of D. polymorpha to thrive as an invasive organisms, including mechanisms of shell formation, the generation of byssal thread attachment fibers, and responses to thermal stress. The D. polymorpha genome provides a rich resource for invasive species research and control efforts.