The Western Antarctic Peninsula (WAP) is a highly productive area of the Southern Ocean, but experiencing rapid warming as a result of global climate change. Subsequent alterations in algal community composition may affect the share of grazing to viral lysis and therefore the mode of carbon and energy transfer through the food web. However, insight into the importance of viral activity within the Antarctic pelagic food web is still very limited and to our knowledge no seasonal study has been executed on viral lysis rates. During two Austral productive seasons (Nov-March) the temporal dynamics of virus and their microbial hosts was describe in relation to key physicochemical parameters. Weekly experiments were conducted to determine viral lysis rates of the different phytoplankton groups, which were compared to the more traditional loss factor grazing that was determined simultaneously. Despite clear intra- and inter-seasonal differences that were observed for phytoplankton (assessed by flow cytometry and pigment fingerprinting), all phytoplankton groups displayed considerable virally induced mortality. Viral lysis rates were comparable to grazing (i.e. on average around 0.3 per day). Our results double the currently existing data set, and clearly indicate the importance of viral infection and host lysis even under very cold conditions as found in Antarctic waters.