Understanding the molecular mechanisms underlying physiological adaptations in marine species is crucial for assessing their resilience to environmental stressors. The Southern King Crab (Lithodes santolla), an ecologically and commercially important species in sub-Antarctic waters, inhabits dynamic fjord ecosystems characterized by fluctuating salinity and oxygen levels. However, the molecular basis of its adaptive responses remains largely unexplored. In this study, we assembled the first de novo transcriptome of L. santolla to characterize gene expression related to osmoregulation and oxidative stress. Gill samples from individuals collected at two sites: Ballena Sound and Choiseul Bay in the Strait of Magellan (Punta Arenas, Chile), exhibiting different environmental conditions. Sequencing yielded 731,879,912 clean reads, which were assembled into 210,093 transcripts, of which 56,064 contigs successfully annotated. Differential expression analysis identified 4,474 differentially expressed genes (DEGs), with individuals from Ballena Sound exhibiting upregulation of heat shock proteins (HSPs) and Na+/K+-ATPase (NKA), suggesting an osmotic stress response. Conversely, individuals from Choiseul Bay showed increased expression of Na+/H+ exchanger (NHE), V-type proton ATPase (VPA), and antioxidant enzymes, indicating regulatory strategies for salinity adaptation. Gene Ontology and KEGG enrichment analyses further highlighted key pathways involved in ion transport, oxidative stress mitigation, and energy metabolism. This study enhances our understanding of L. santolla’s physiological plasticity and provides a valuable molecular framework for future research on environmental resilience and conservation of sub-Antarctic marine species.