<p>Gill function in gas exchange and ion regulation is crucial for ionoregulatory homeostasis in teleost fishes, yet further research is needed to elucidate how cold stress affects these processes, particularly in relation to salinity-dependent tolerability. Indian medaka (<i>Oryzias melastigma</i>) were acclimated to freshwater (FW) and seawater (SW) environments before being exposed to cold stress at 18 °C for 168&#xa0;h. The protein abundance of the apoptotic marker Caspase-3 increased significantly in SW-acclimated fish compared to controls, indicating a heightened apoptotic response under cold stress in SW conditions. Concurrently, the expression of the anti-apoptotic gene <i>birc5</i> exhibited distinct patterns in FW and SW, suggesting differential regulatory mechanisms in response to cold exposure. Transcriptomic analysis revealed that cold stress significantly influenced genes related to ion regulation, osmoregulation, and cellular metabolism, with distinct pathways activated in FW and SW environments. Notably, SW-specific genes were predominantly involved in metabolic pathways and stress signaling, while FW-specific genes were linked to transport processes and cellular maintenance. Additionally, cold stress significantly affected the expression of Na⁺/K⁺-ATPase (NKA) subunits and ion transport genes, underscoring the impact of temperature and salinity on gill function. The study highlights the importance of tight junctions (TJ) and gap junction (GJ) in maintaining gill integrity during environmental stress, with differential regulation of key genes like <i>ocln</i>, <i>cask</i>, and <i>gja3</i> in response to salinity and temperature shifts. These findings highlight the superior molecular and cellular adaptations of euryhaline fish in SW to cold stress, emphasizing how salinity enhances gill responses and suggesting potential strategies for improving cold tolerance in aquaculture.</p> Graphical Abstract <p></p>