Global change and the associated increase in temperature raise serious concerns for the conservation of Antarctic marine biodiversity, which is particularly vulnerable due to the stenothermal nature and highly specialized adaptations of its fauna. Trematomus bernacchii (commonly named emerald rockcod), a Southern Ocean-endemic benthic fish, serves as a valuable model organism for investigating the molecular and physiological impacts of climate change in polar ecosystems. Transposable elements (TEs) are of particular interest, as they are known to become activated under stress and to influence genome plasticity and gene regulation. In this study, we examined the transcriptional response of TEs and their silencing mechanisms in the gills and liver of T. bernacchii specimens exposed to thermal stress (+ 1 °C and + 3 °C compared to a 0 °C control) for 5 and 15 days. Our results showed that temperature increase triggered a transient activation of TEs, followed by the upregulation of silencing-related genes, including members of the Argonaute family, heterochromatin-associated factors, and components of the NuRD complex. Tissue-specific patterns were observed: the liver exhibited a rapid balance between TE activation and silencing, indicating a coordinated and resilient response, while the gills showed a sustained upregulation of both TEs and silencing genes, likely due to their greater sensitivity to environmental changes. These findings highlighted a complex, dynamic interplay between TEs and their regulatory systems under heat stress, offering new insights into early adaptive responses and potential resilience mechanisms in a cold-adapted species facing climate-induced biodiversity loss.