BACKGROUND: Antarctic marine organisms have evolved a variety of physiological, life-history and molecular adaptations that allow them to cope with the extreme conditions in one of the coldest and most temperature-stable marine environments on Earth. The increase in temperature of the Southern Ocean, product of climate change, represents a great challenge for the survival of these organisms. It has been documented that some Antarctic marine invertebrates are not capable of generating a thermal stress response by means of an increase in the synthesis of heat shock proteins, which could be related with their low capacity for acclimatization. In order to understand the role of heat shock proteins as a compensatory response in Antarctic marine species to projected scenarios of increased seawater temperatures, we assessed the expression of the genes Hsp90, Grp78, Hyou1 and Hsc70 in the Antarctic sea urchin Sterechinus neumayeri under three thermal treatments (1 °C, 3 °C and 5 °C), for a period of exposure of 1, 24 and 48 h RESULTS: The results obtained showed that these genes were expressed themselves in all of the tissues analyzed in a constitutive form. During acute thermal stress, an overexpression of the Hsp90, Grp78 and Hyou1 genes was observed in coelomocyte samples at 3 °C after 48 h, while in esophageal samples, an increase in Hsp90 and Grp78 expression was observed after 48 h. Thermal stress at 5 °C, in general, did not produce a significant increase in the expression of the genes that were studied. The expression of Hsp70 did not show modifications in its expression as a result of thermal stress CONCLUSIONS: S. neumayeri is capable of overexpressing stress proteins as a result of thermal stress, however, this response is delayed and to a lesser degree compared to other Antarctic or temperate species. These results indicate that adult individuals could cope with the expected impacts caused by an increase in coastal sea temperatures in the Southern Ocean.