The Eurasian perch (Perca fluviatitis) is the most common fish of the Percidae family widely distributed across Eurasia. Perch is a popular target for professional and recreational fisheries and promising freshwater aquaculture species in Europe. However, despite of its high ecological, economical and societal importance, the available genomic resources for P. fluviatilis are lagging behind. Here, we report de novo assembly and annotation of the whole genome sequence of perch which is expected to facilitate exploitation of genomic information for ecological and evolutionary research, selective breeding programs, sustainable fisheries management and conservation.