Direct studies of long-term RNA virus evolution are largely limited to chemically-fixed specimens from natural history and pathology museums collected over the past two centuries. Detecting genomic traces of RNA viruses in older, buried remains is generally considered highly unlikely. The cold, dry conditions of Antarctica may represent an exception. Under such circumstances, natural mummification of penguins and seals—animals that form large colonies where RNA viruses circulate—is common and may facilitate the recovery of RNA virus genomes. Here, we show that Adélie penguin ( Pygoscelis adeliae ) mummies, ranging in age from recent to nearly two millennia, indeed contain fragments of such ancient viral genomes. Metatranscriptomic analyses yielded near-complete genome sequences of a picornavirus ( Megrivirus epengu ) and a rotavirus D ( Rotavirus deltagastroenteritidis ) from relatively recent specimens. We further retrieved rotavirus D sequences from a 280-year-old individual and a near-complete rotavirus G ( Rotavirus gammagastroenteritidis ) genome from a 1900-year-old one. These findings pave the way to direct studies of RNA virus evolution across millennia. ### Competing Interest Statement The authors have declared no competing interest. Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Transregio Collaborative Research Centre 410 “WETSCAPES2.0”, Project-ID 531801029 – TRR 410 National Science Foundation, ANT 1443386, OPP 9909274 US National Institutes of Health, R01 AI153044 Research Foundation - Flanders (‘Fonds voor Wetenschappelijk Onderzoek - Vlaanderen’, G0D5117N, G0B9317N, G051322N Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Germany's Excellence Strategy - EXC 2155 - project number 390874280 Helmholtz Association’s Initiative and Network Fund, KA1-Co-02 “CoViPa”