Milkfish (Chanos chanos) is one of the most important aquaculture species in Asian countries. These teleost fish are traditionally cultured in outdoor-based systems and therefore have to cope with daily and/or seasonally changing environmental conditions. Temperature changes beyond the optimal range of a species are known to induce an endocrine stress response through activation of the hypothalamic-pituitary-interrenal (HPI) axis, hereby triggering the release of cortisol in order to regain homeostasis. The pertinent literature on milkfish lacks data on chronic stress, however, long-term elevations of cortisol are known to be detrimental for the fish performance. This study is the first on chronic stress in juvenile milkfish quantified by using ontogenetic (OG) and regenerated (RG) scale cortisol. We analyzed scale cortisol of juvenile milkfish, which were exposed to a gradual temperature increase of 1 degrees C per day in the range from 26 degrees C to 33 degrees C, followed by an exposure to constant 33 degrees C for 21 days. Significant higher RG scale cortisol concentrations were observed in juvenile milkfish exposed constantly to 33 degrees C, compared to milkfish kept at 26 degrees C. Even the gradual temperature increase from 26 degrees C to 33 degrees C over 7 days resulted into higher OG scale cortisol concentrations. Although milkfish showed reduced growth in the first 7 days at 33 degrees C, overall fish growth was positively affected by higher temperature. As anthropogenic activities affecting the climate are increasing, and taking into account the widespread use of outdoor aquaculture systems, which are prone to natural fluctuations, an increase in temperature is most likely to be considered a stressor in milkfish aquaculture, as indicated by our results. Hereby, the use of scale cortisol was shown to be effective to quantify even minute and gradual temperature changes, making it a powerful tool in optimizing aquaculture systems as well as in monitoring gradual climate changes in wild stock.