Antarctic waters are a particular marine environment mainly due to the strong seasonal variations that various parameters are subject to, like light availability and temperature. As in all oceanographic regions, food webs are sustained by photosynthetic microorganisms, which in the case of Antarctic environments seem to be strongly dominated by its eukaryote component. Assessing the ecological role of photosynthetic microbial eukaryotes requires a basic knowledge of their diversity and community composition. This review integrates the available information regarding this component of Antarctic phytoplankton as a way to unveil its diversity and how they respond to the strong changes that occur in this environment. Although several studies indicate the presence of a highly endemic biota in Antarctica, data sets on marine photosynthetic eukaryotes diversity suggests that endemism may be strongly influenced by the low coverage that Antarctic marine areas have been subjected. Moreover, most studies demonstrate that climate change is occurring faster than expected, especially in the Antarctic Peninsula and that this could result in a significant loss of global microbial biodiversity. The changes that eukaryote phytoplankton experience due to this phenomenon may have strong repercussion on the food webs in the Southern Ocean. The knowledge of both the diversity and variation of marine eukaryote phytoplankton in Antarctic waters is crucial for the proper understanding and predictability regarding how these environments can respond to a changing ocean.