During a 2019 Chilean Antarctic Scientific Expedition (ECA 55) studying crustose coralline algae (CCA) diversity on the Antarctic Peninsula, bleaching of these algae was observed for the first time in this region. Here, we present initial findings on the physiological state of bleached and normally pigmented CCA (Clathromorphum sp.) assessed using chlorophyll-a fluorescence induction pulse amplitude modulation. The study site experienced high light exposure and salinity in the water column. Our analyses found that bleached CCA have relatively healthy photophysiology responses but lower photosynthetic efficiency, which could be associated with the low salinities recorded in the study area. However, seasonal monitoring and mesocosm experiments across the southern polar latitudes are urgently required to confirm this hypothesis.