Whether phytoplankton mortality is caused by grazing or viral lysis has important implications for phytoplankton dynamics and biogeochemical cycling. The ecological relevance of viral lysis for Antarctic phytoplankton is still under-studied. The Amundsen Sea is highly productive in spring and summer, especially in the Amundsen Sea Polynya (ASP), and very sensitive to global warming-induced ice-melt. This study reports on the importance of the viral lysis, compared to grazing, of pico- and nanophytoplankton, using the modified dilution method (based on apparent growth rates) in combination with flow cytometry and size fractionation. Considerable viral lysis was shown for all phytoplankton populations, independent of sampling location and cell size. In contrast, the average grazing rate was 116% higher for the larger nanophytoplankton, and grazing was also higher in the ASP (0.45 d−1 vs. 0.30 d−1 outside). Despite average specific viral lysis rates being lower than grazing rates (0.17 d−1 vs. 0.29 d−1), the average amount of phytoplankton carbon lost was similar (0.6 µg C L−1 d−1 each). The viral lysis of the larger-sized phytoplankton populations (including diatoms) and the high lysis rates of the abundant P. antarctica contributed substantially to the carbon lost. Our results demonstrate that viral lysis is a principal loss factor to consider for Southern Ocean phytoplankton communities and ecosystem production.